The Maddest House, by busaikko. Slash, Sirius/Remus. (ca. 42,700 words)
In this AU Remus and Sirius raise Harry. Also Voldemort's spirit remains in Britain after Halloween 1981 rather than fleeing.
The If Sieve, by Cathy. Slash, Harry/Draco. (ca. 36,000 words)
Draco goes through potential alternative universes with a pensieve-like device, exploring what would have happened if he (or Harry) had made different decisions. It's a cool magical device and the scenarios are HP fandom staples, but handled in an original way, often with not quite the expected outcome. (also on AO3)
Catechism, by dreamfall. Gen. WIP
I'm not that much into the extreme end of the "Harry was abused by the Dursleys" genre, but this one is rather clever in that it asks what might have been had the Dursleys taught Harry to hate magic.
Dark Lord of Azkaban, by Fantome. Gen. (ca. 8,400 words)
In this AU Tom Riddle was arrested for letting the Basilisk loose and killing Myrtle, but he hasn't given up on his ambition to become a Dark Lord, and after several years in Azkaban he sees and opportunity in the ministry inspector Peter Pettigrew...
Blood Magic, by GatewayGirl. Mostly gen, though there's some Severus/Remus slash.
I admit that as a genre I'm not that fond of "Snape-is-Harry's-father" stories -- actually my first reaction to discovering that there's a vast subgenre of this in HP fanfic was "wtf?!" but Blood Magic convinced me that this scenario can be done really well. It's a long, satisfying read (it has 83 chapters) with a plausible backstory for how Snape could be Harry's father and why/how James and Lily covered that up, it has an engaging plot with both character development and some action/adventure elements, and interesting theories about magic and how it works in the HP universe.
Power, by Gatewaygirl. Slash, Harry/Draco.
It's a Slytherin!Harry AU, basically it's a story about after Quidditch sex, but also an interesting glimpse of the characters in a universe where Harry wasn't afraid of ambition and power, and thus Draco isn't a bully, but rather bullied.
Scenes from Another Life, by Helene. Slash, Remus Lupin/Sirius Black.
Harry talks with Ron on their first trip on the Hogwarts express and tells him about his life and of having been raised by Remus and Sirius.
The Only One He Ever Feared, by J.J. Taylor. Gen.
It's hard to describe this fic without giving away too much, but you should give it a try even if you usually dislike stories suggesting that Dumbledore might be a bad guy. It is deliciously creepy and messes with the reader's mind.
Five Ways Remus Lupin Never Raised Harry Potter, by Juliette Kelley. Slash, Remus/Sirius. (ca. 5,300 words)
Each of the five scenes branches of at a different point in canon.
Dudley Dursley and the Hogwarts Letter, by Kindkit. Gen, Dudley Dursley, Lily Potter, Harry Potter, James Potter. (ca. 1,940 words.)
This story gives a brief but interesting look at who Dudley might have become had the Dursleys died in a car crash and the Potters survived. (also on AO3)
Accio Stone, by KrisLaughs. Slash and het, Sirius/Remus and James/Lily. (8,800 words)
Lily and James survived Voldemort's attack, though not completely unscathed, and Harry grows up with them. The story takes place on Harry's eleventh birthday, and of course there's Voldemort trouble.
Sacrifices universe (The individual novels are Saving Connor (ca. 74,800 words), No Mouth But Some Serpent's (ca. 146,300 words), Comes Out of Darkness Morn (ca. 264,600 words), Freedom and Not Peace (ca. 627,000 words), and Wind That Shakes the Seas and Stars (ca. 993,100 words), A Song In Time of Revolution (ca. 908,600 words), and I Am Also Thy Brother (ca. 697,700 words), by Lightning Wave. Slash, Harry/Draco in the later novels.
The story's premise of Harry having a twin brother, with both of them and their family surviving, and later Harry being sorted into Slytherin and his brother into Gryffindor sounds like a wacky badfic, but it isn't. True, if you read strictly for canon characterization you should skip this AU, the characters are sometimes quite far from what we see in the books, and I have especially problems with this view story's Dumbledore and Lily. It twists the characterizations in a deus ex machina way, but they're not ridiculous or caricatures, either. That said, this is an immensely entertaining and satisfyingly long read. Once I started it had me hooked, and I couldn't put it down, what with its length presented some problems, but was totally worth it. This series of novels have a great plots, very cool, imaginative ideas and descriptions of magic, rituals and wizarding customs, a Powerful!Harry (which I really enjoy), Snape as Harry's mentor (another thing I like), and overall the deviations from the canon characterizations led to character interactions and plot elements I enjoy, so I don't mind that they're not like in the books. (also on ff.net)
Two Households, Both Alike In Dignity, and its sequels Two Households II: Two Weeks Over Easter and Two Households III: Growing Pains, Two Households IV: Busman's Holiday and Two Households V: Mortal Flesh by Mad Martha. Slash, Harry/Ron.
It's a Slytherin!Harry AU, but it stands out among that genre, not at least because here Harry being sorted into Slytherin doesn't result in him being on good terms with Draco, and Ron-bashing is notably absent.
Sorted Differently, by Mags. Gen, Harry.
This is a short humor ficlet that shows three ways the sorting could have been different. Not that the first years are sorted into houses different from canon, it's that it's not a hat doing the sorting.
Oscillate Wildly, by Marks. Slash, Harry/Draco.
This novel adapts the idea of the Buffy episode "Normal Again" (where she's been in an asylum since high school, and only imagined the reality as Slayer) to the HP universe. Here Harry is stuck between two lives, one at Hogwarts and one in a mental institution, and has to try to find out what's real and whom to trust.
If You've A Ready Mind, by Maya. Slash, Harry/Draco, Draco/Terry, also het, Draco/Cho.
Draco is sorted into Ravenclaw in this AU. It is from Draco's POV and very funny in places, though as with the books things get darker as time progresses. Still overall the story is on the lighthearted side and made me laugh frequently. (Sadly, I don't have a working link to the story anymore.)
No Way Back, by Meri. Slash, Snape/Harry. (ca. 77,780 words)
It has the same premise as Midnight Blue's Mirror of Maybe, i.e. that Harry gets sent through a magical mirror, gaining experience during an alternate life before coming back, but deals with it differently. (also on AO3)
Five Things That Never Happened to Petunia Dursley, by November Snowflake. Gen. (ca 1,200 words)
This is a cool look at Petunia and how her life might have been. Well worth reading even for those who aren't especially interested in her character. (also on AO3)
Same Time, Next Year, by Olivia Lupin. Slash, Harry/Draco.
There are plenty of stories where Harry gets sorted into Slytherin, but what if Draco had become a Gryffindor? Admittedly, at first I was a bit skeptical about the premise of Gryffindor!Draco, but the way it was handled made me suspend my initial disbelief for the duration of the story. And the format of showing just the first day each year and the way the author mixed in the events from the books worked beautifully for me. It gave a sense of the whole alternate universe without tediously retelling events in a merely slightly modified version as so many of the "sorted in a different house" AUs are prone to do.
The Curious Incident of the Dog in the Night-Time, by Penknife. Slash, Remus Lupin/Sirius Black. (ca. 6,100 words)
The author describes it as "Harry Potter meets Jane Eyre meets Penknife's brain on crack" but the Gothic setting works great with Sirius and his creepy family. I really enjoyed the atmosphere of this AU. (needs AO3 account)
Bringer of Death, by P.L.S. Gen.
This AU proposes a different interpretation for the prophecy from OotP, one where neither Harry nor Neville are marked by Voldemort's killing curse, and Voldemort didn't vanish. Also Dumbledore is somewhat more ruthless than in the books. I found the scenario quite original, if a bit on the far side of canonically possible character interpretations. Also the story has some spelling errors, so if typos are among your pet peeves you might get annoyed.
Grim Dawn, by RobinLady. Gen.
It's a "what if..." scenario: Harry meets Sirius before he gets on the Knight Bus in PoA. I know that to have Sirius "rescue" Harry and then prove his innocence is one of the standard plots in HP fanfic, but this one stands out among its genre.
Reclamation, by Sam Vimes. Mostly gen, though Sirius/Remus is implied.
What if Tom Riddle had not become Lord Voldemort, stopped his descent before it became irrevocable, and instead taught DADA at Hogwarts?
Stealing Harry, and its sequel Laocoon's Children (First and Second Year of Laocoon's Children are finished, the rest is still a WIP), by Sam Vimes. Slash and het, Sirius/Remus and Snape/Tonks, though it's not focused on the couples or romance.
In this AU the events of that fateful Halloween night unfolded somewhat differently. As a result Sirius never went to Azkaban, Lucius Malfoy did, and though Harry first ended up with the Dursleys, Sirius gets custody of him when Harry's eight. Sirius and Remus have to protect him from Pettigrew and Voldemort, Snape interferes, Harry ends up in Slytherin (not to mention Draco in Hufflepuff, with a backstory that even might make you believe this possible when you squint), and of course there are pranks and adventures, too. (also on AO3)
A Time To Change and its sequel Betrayal Can Only Happen If You Love, by Sansa. Slash, Harry Potter/Severus Snape. (ca. 75,500 and 87,100 words)
The story is about multiple timelines and since it starts from the canon one, I guess some don't count it as AU, however for me the alternative timelines work effectively like one. Harry wishes that he had never been the Boy-Who-Lived and now has to bear the consequences. What I really like here is that not everything gets better, and he didn't really think about the consequences of his seemingly benign wish at first, and how his attempt to fix things with time travel is handled here is fascinating. (the first also on sycophanthex)
House Colours, by Sarka. Slash, Harry Potter/Draco Malfoy. (ca. 12,800 words)
This is a Slytherin!Harry with Gryffindor!Draco AU, and I really enjoyed it, not least because it had a Ron who was first friends with Draco and then Harry, rather than the Ron-bashing that is so depressingly common in Slytherin!Harry stories.
And death shall have no dominion, by Snakeling. Slash, Harry Potter/Severus Snape.
Snape didn't survive his encounter with Remus in the Shrieking Shack. He remained as a ghost bound to Hogwarts and becomes friends with Harry who has been sorted into Slytherin. (also on AO3)
When It Alteration Finds, by victoria p. Gen and slash, Remus Lupin/Sirius Black, Remus Lupin/Severus Snape. (ca. 7,300 words)
These are four vignettes, each placing Remus in a different Hogwarts house. (also on AO3)