For TS the links are sorted by the type of the AU (see sub-categories) in addition to being sorted by author, but in the end I was too lazy to adopt that system for the other fandoms that have accumulated many entries. It is marked whether something is gen, slash or het, but those are not separate sections.
Detour, by Emily Brunson. Slash, Jim/Blair. (311 K)
You probably have read this one already, it is the classic TS AU, so even if everybody knows it, I would never skip it on an AU rec page. It explores what would have happened, if Jim hadn't gone to visit Blair during the pilot, and is simply awesome. (Currently there's no link available, as Emily Brunson's site is being reorganized, however you can find it in the files section of her Yahoo!Group EmLand.)
Aphrodite's Garden, by Emily Brunson. Slash, Jim/Blair. WIP
If I just tell you the premise "Jim as a hooker", it wouldn't do this story justice, because it's not a kink story that bends the characters into an unlikely situation, but Em makes you believe their lives could have happened that way, even if hooker stories usually don't do much for you. (Currently there's no link available, as Emily Brunson's site is being reorganized, however you can find it in the files section of her Yahoo!Group EmLand.)
Coming Up for Air Series, by Delilah. Gen.
I found the first story thanks to Kathryn's reviews. In this AU Jim never suppressed his senses as a kid, but unfortunately they were treated as a mental illness. I really liked that the scenario unfolded in a way that meeting Blair does not 'fix' Jim. It's more plausible, though a bit depressing. It's from told Blair's POV, which works very well given Jim's condition, but I couldn't help to wonder how Jim perceives the events. So after reading the first I wished for a sequel or a companion piece, and when the second was published I liked it as well (though it's still from Blair's POV). So now I'm hoping that this universe will be continued for some time, a sure sign that the AU works for me: I don't want to leave <g>.
Primates, by grit kitty. Pre-Slash. (9,612 words)
Jim and Blair meet a little later than in canon, around the time when Blair's apartment blew up because of the drug lab (and it seems the Switchman case didn't happen)... But what makes this AU different and what I really enjoyed was that Blair doesn't recognize Jim as a sentinel on sight, that we don't see Blair doing the whole "there was this guy Burton, the explorer not the actor, who wrote a monograph about how every village had a sentinel" routine yet again, that they don't think meeting the other has special significance at first, even though Jim is struggling with the new quality of his senses throughout the story. (needs an AO3 account to read)
Outside These Walls, by Jael Lyn. Gen. (29,470 words)
Obviously I'm a sucker for the classic "Jim and Blair meet at a different time" AU, but this one was a refreshing take on the theme. Jim doesn't end up in a psych ward, just because he doesn't meet Blair when his senses resurface. He has problems (and the story has some nice parts dealing with the senses), but he is resourceful and copes with them.
Jungles of Peru, by Jaguar. Gen. WIP
Jaguar's TS fiction page (which afaik was last found at www.jag.cx/Sentinel/FanFiction.shtml) doesn't seem to be working at the moment. :( I hope the story will be online again one day, and if that happens, I'll link it. (ETA: I found a link to the first two parts of it on the WayBackMachine, part 1 and part 2) I'm fond of the "what if Jim hadn't been rescued" genre, as is obvious on this rec page. But every author has a different take on that subject, and this one is well worth reading. Jim has been staying in Peru now for nearly eight years, with no intention to leave, adapted a lot to the Chopec way of life, and accepted his senses, when he meets Blair, who's on an expedition into Chopec territory with some students.
The Jungle Book, by Katrina Bowen. Slash, Jim/Blair.
A classic of the genre "what if Jim hadn't been rescued after 18 months?", and still one of best. The Peruvian jungle, Jim, Blair... and best of all, this one has a plot to sustain it.
The web version of this zine story isn't available right now, because the author's page is down. It was at trickster.org/adoratrice/jindex.htm, but unfortunately in the Wayback Machine archives the last chapter is missing. The non-expanded, earlier online version is still available as In The Jungle (2,364 words) and Beyond the End (20,968 words) though.
Behind Bars, Mia Athlas. Slash, Jim/Blair. (39,638 words)
Jim and Blair don't meet like in canon, but in prison. Blair's there because of his date with Iris not ending so lucky, and Jim, well, that would spoil it, but I bought the story, mostly. I would have preferred a different outcome and you shouldn't come to this story for a totally realistic look at the justice system, but then the way things work in TS canon aren't reality tv to begin with, and this story works if you view it in that light. What can I say, I have a thing for prison fiction, and the senses play a noticeable role too, which I always like in TS stories.
Footpaths Through Peru Series, by Rivanna. Gen.
Another one where Jim and Blair meet in Peru, this time with Jim Ellison still an Army Ranger and Blair as an undergraduate. After a long wait the fifth story in this series, The Wings of Faith, was finally posted. So everybody who avoids reading WIPs is now in for the treat of reading all five stories in a row. The only bad thing is that Rivanna announced that this would be her last TS story.
Miracles Of Life, by D.L. Witherspoon. Gen, though Jim/Alex is mentioned. (160 K)
This is one of those stories, where upon hearing the summary you think they must surely suck, and then it turns out that they don't. Alex is pregnant, Jim is the father, in the end he and Blair raise the kid. It is not my favorite thing for a TS plot, and I'm not too keen on stories with the heroes raising kids (which is why I didn't like the sequels as much), but the first story has a compelling scenario that deals with the implications of the "mating instinct" the two sentinels displayed in canon during S2. It has some of the weaknesses most of D.L. Witherspoon's stories share, though, for example the inane exposition dump with some bare bones character basics at the beginning, which is extremely redundant in especially fanfic.
Imperfections Series, by Dasha. Gen.
So far there are four parts, Imperfections (149 K), and its sequels Imperfections II: Believing in Fairy Tales (158 K), Imperfections III: Visiting (100 K) and Imperfections IV: Necessary Parts (189 K). It's another version of the popular AU theme of "What if sentinels were known?" but the focus is less on the universe building and more on their partnership. Also there are no special psychic "guide powers" nor has modern society developed really strange customs, instead there is a refreshingly pragmatic and contractual view of the working relationship between sentinels and their partners. As often in Dasha's stories there are lots of sensory and sentinel details, but no rehashing of boring fanon phrases. The series is also a crossover with other shows, but the other shows don't play a large role, it's almost a bit like character cameos.
If I Run Far Enough, by Dean Warner. Slash, Jim/Blair. WIP
This story isn't linked, because the last URL I knew (Dean's Writing Nook) vanished when nbci.com/xoom.com stopped their free webservices. And though Dean's Page is online again at deanfic.slashdom.net, I couldn't find the WIP anymore. But I still hope it will be on the web again one time, because even though very little has been added to this fascinating AH since I came into TS fandom, it is still one of my favorite takes on the theme of "what if sentinels were known", and although by now there are plenty of stories with such premises, I think it was one of the earliest, if not the first of its kind. And it is a well developed Alternate History as well, where WWII, the Korean War and the following history turned out to be very different from the Cold War in our reality, so this has a solid SF background that really pulled me in. If anybody sees it online again (or published in a zine somewhere), please e-mail me.
Conjugations, by Legion. Slash, Jim/Blair. (54,778 words)
Well, it is a sort of an AH, there is a plague, things deteriorate, and slowly end up in a sort of neo-tribal setting, but some people, among them Jim and Blair are still remembering the old times while adjusting to the new... First the positive things, it is a basically interesting SF premise, the initial idea for the plague and its immediate consequences is neat, the writing is overall sound, and it has a substantial plot, plus I like long stories, so it's well worth a rec, however I also had several problems with this one. First the past and future generations were woven together in a (at least to me) somewhat confusing way, and I had some problems with the later plot, especially the part where the (reborn?) Jim and Blair are fighting guttural speaking Russian hordes who come across the Pacific raping and pillaging the peaceful utopian North American tribes, which are living in harmony with nature, supposedly just because they don't have enough enough space and natural resources in all of Eurasia. And that even though with before the catastrophe probably even fewer of the people there had the anti-allergy medicine when the dying started, thus the death rate through all of the poorer regions must have been much higher than in the US, and those areas even more depopulated, and generations later North America is still mostly empty because of infertility and a collapsed birthrate... So at some point my suspension of disbelieve just snapped. If there are more detailed explanations, I want them to be more plausible. (needs an AO3 account to read)
Sentinel-Guide Research Project, by Sorka. Slash, Jim/Blair. (41,202 words)
Another one in the genre of "what if sentinels were known", and the author says it was written in reaction to Susan's GDP series, but IMO it works better than that one. What it would have needed is a more thorough proof-reading for typos etc. (at least the version I read at the archive) but I can overlook such problems for a captivating story, and this one certainly held my interest. (needs an AO3 account to read)
Night Watch, by Brighid. Slash, Jim/Blair. (6,616 words)
Jim is head of EllisonCorp at day and vigilante at night... I was a bit surprised how well the universes meshed in this Batman-TS fusion, since for me both have a very different feeling and tone. The Batman universe in my mind is a very dark place, because the only Batman comics I've read are along the lines of Miller's The Dark Knight Returns, Year One (Miller/Mazuchelli), The Killing Joke (Moore/Bolland), and Arkham Asylum (Morrison/McKean). I never watched the tv series and I can't remember seeing any movie (though I might have). Whereas the TS universe for me is a friendlier place. But right the first scene which sets the background of the "Night Watch" pulled me in and made me feel like in a Batman comic. Another thing well managed were the senses, because for my view of Batman it is crucial that he has no super powers, but somehow because of the double-edged nature of the senses they were incorporated without making Night Watch more of a superhero with powers and less a human vigilante. And I'm still waiting for the promised next installment, Switchman vs. Night Watch.
Inclination, by Laura Jacquez Valentine. Slash, Jim/Telar. (18,210 words)
A Star Trek TS fusion, with 'Blair' as the Vulcan Telar. The characters are not quite like they are in 'regular' TS, but that's to be expected with Blair as a Vulcan, and the reasons for the differences in characterizations are sound and not arbitrary, which is what matters to me in an AU. This story does some fascinating things with Vulcan culture, but I'd have really liked to see more of why and how enhanced senses are useful on a Starfleet ship, with all their sensors, their empaths to detect hidden intentions etc. What does make a sentinel so valuable for Starfleet that they specifically train guides? And how does Jim use his senses? The story focused a lot on this AU's version of Vulcan and Blair's situation and that was fascinating, but there could have been more stuff about the senses in it. Still definitely worth reading.
There Is No Gene, by T'Mar. Slash, Jim/Blair. (8,181 words)
A fusion between Gattaca and TS. (needs an AO3 account to read)
Destiny's Bond, by Wolfling. Slash, Enqueri/Blair. (40,093 words)
It's the SG-1 universe, Blair is recruited for one of their teams by Daniel, and on P8-935 Blair meets his destiny, the sentinel Enqueri. I liked how this AU explored how Jim might have accepted his senses in a radically different environment. I'm not that enthusiastic about the direction the sequel (still a WIP) is taking, but but you can check out Destiny's Choice on Wolfling's TS page.
Love Amidst the Ruins, by boyd. Slash, Jim/Blair. (18,697 words)
A post-apocalyptic setting, SF-action-adventure with Jim and Blair in leather gear fighting in a jungle against aliens with the help of high-tech gadgets and a telepathic bond that also includes a battle cat... it sounds totally cheesy, and yet the story is well written fun, the descriptions vivid and the setting interesting, so that I suspended my disbelief and got pulled into this bleak world. The initial exposition parts may be a bit too concentrated for some, but I love world building, so I had no objections to them.
Roachia Series, by Cindy L. Combs. Gen.
I like SF, I like TS, and the two fit quite well in this SF action adventure with sentinel senses. Humans are fighting the insectoid natives of the planet their ship crashlanded upon, and they're loosing, when an untrained sentinel brings the humans back an advantage they have long thought to be extinguished in the Roachians attacks... Put like that, it sounds a bit like a 1930's pulp magazine, but it is certainly a fun action-adventure in the spirit of TS. You have explosions, fight scenes, great characters, sentinel senses, all in a solid SF setting.
The Measure of Our Youth, by Debra Fran Baker. Slash, Jim/Blair. (21,182 words)
It's 1969, Jim is a history professor, Blair a Vietnam veteran, and this story made that time come alive for me. (Also available on AO3, but needs an account to read there.)
Night Eagle and its sequel Night Eagle: Homecoming, by Donna Gentry. Gen.
This series is set in America's old west, has great sentinel scenes (for example how the visualization control might work without people being familiar with things like 'dials') and is very evocative of the time. The best Western AU I've read in TS so far. (Unfortunately its now only available through the Wayback Machine, afaik.)
My Soul To Keep, by Donna Gentry. Gen. (363K)
Another post-apocalyptic AU (I do have a fondness for that genre...) and it has has an intriguing premise: Sentinels are known, but there are no guides anymore, until they find a frozen Sandburg, the remnant of some long forgotten pre-war project... The writing is good, and one gets glimpses of a full SF-like setting, unfortunately the story never realizes its full potential. We don't see a lot of the universe, and the plot and character development aren't so much used to explore the consequences of the AU premise, but rather constructed to let them end in a familiar, all too predictable place. However, the exploration of how Blair deals with being awakened from cryogenic sleep, and how Jim and Blair meet and get to know each other is well done, and I enjoyed reading it enough to rec it, though it's not my favorite of Donna's stories. A sequel with a focus on the more SF-like aspects of the universe would be great, but then I'm always hoping for more stories by this author. (Unfortunately its now only available through the Wayback Machine, afaik.)
Prison, by Jack Reuben Darcy. Slash, Jim/Blair. (87,385 words)
It's set in Singapore 1937, thus the mutual angst about their relationship is much more believable than it would be in Cascade during the 1990s. The changes in character are founded in the setting, the descriptions are compelling, and the story gives the senses a central role, and not just telling us that Jim is a sentinel, but making the senses come alive.
Nature Series, by Francesca. Slash, Jim/Blair. Individual stories are finished, but the universe is still a WIP.
A magnum opus, a true classic, everybody will have read it already anyway, so why am I still reccing it? Because it is the most elaborate alternate version on how the sentinel senses work and will ultimately develop that I have found so far. It puts a much greater emphasis than TS canon on shamanistic and Guide (with capital G) things, but that's fine, because it is consistent in its version and very well written. And I shouldn't forget to mention that it also draws a vivid picture of how their relationship might develop. And when you're through with the three arcs and their 29 stories that are published so far, don't miss the Cycles Series, with a look from 50 years in the future back on our favorite duo.
Guardians of the Tribe Series, by Lori. Slash, Jim/Blair. Individual stories are finished, but the universe is still a WIP.
I could have put this into the "change of character" category, but that Jim is a shapeshifter who can become a black jaguar isn't the only thing that's different in this universe (as it progresses it becomes clear that there are forms of magic, for example). Still, this is not a fantasy setting with wizards and elves but present day, which makes the subtle rule changes all the more effective. I admit that Jim as a panther stories really push my buttons, and additionally this has D/s undercurrents (in a non-roleplay setting) which I also like a lot, so I'm biased in favor of the series. But this one is definitely my favorite in the shapeshifting genre, it has some great scenes, some of them really funny too, and it has a underlying backstory about the positions of shapeshifters in the overall scheme of things, which I'd like to hear more about, but unfortunately there hasn't been a new installment in quite a while.
Sweetcheeks I-X, by Debra Fran Baker. Slash, Jim/Blair.
Jim is gay, in a more flamboyant way than usual, and Blair gives him the opening to get back to his roots and drop the macho routine. Which results in Jim still chasing criminals and wrecking cars, just that he ruins his silk suits along the way. The series starts out as humor, but then takes some darker turns. And the long awaited 10th part, Stitches, is finally published.
The Sound Of Silence Universe, by Mysti Frank. Slash, Jim/Blair. Individual vignettes are finished, but the universe is still a WIP.
(The last URL I have for this, at www.techplus.com/slashvillage/sos/, doesn't seem to be working anymore, if anyone knows if/where it's still available, I'd be grateful for an e-mail.)
It could be argued that this isn't an AU at all but a regular disability fic. But because the cause for Blair's deafness is never explored, even though it probably happens sometime during TS canon, it felt a lot like an AU to me, and it's close enough to the AU genre, that it doesn't feel like cheating to rec it here (which is the only rec page I maintain at the moment). And I enjoyed those vignettes which are dealing realistically (at least to me it seemed that way) with the disability a lot. I don't think the the zine which collects them into one story will ever come out, but this universe stands quite well on its own as it is now.
Nahual, by Peregrine. Gen. (ca. 68,940 words)
Like with Guardians of the Tribe, that I recced above, Jim can turn into a jaguar (yeah, I have a soft spot for those), but unlike in that AU, here nothing else in canon is changed, and at the beginning of the story Jim isn't aware of his ability either. I thought the story handled Jim and Blair dealing with the new weirdness well, and the explanations for the jaguar transformation worked as an extension of the show's mysticism.