Lovers and Dreamers, by Alexia Eve. (64 K)
So it's a Smallville/Muppet Show x-over, but it's also an AU, because Clark and Lex didn't meet in Smallville. And it's not only hilarious, it also truly works. I mean Lionel together with Waldorf and Statler, what more could you want?
Inside Out (ca. 4,250 words) and its sequels Independence Day (ca. 550 words) and untitled snippet (ca. 630 words), by Corinna. Slash, Clark/Lex.
This AU is set in 1969, at the beginning of the Stonewall Riots in New York, and the though the story is relatively short, it has good world building without clumsy exposition. It felt to me like there was more to the characters and their backstory than we glimpse in the story itself, so the AU was made real and three-dimensional. (main story also on AO3)
Mere Mortals, by deanine. (ca. 173,000 words so far) WIP
The story is long, and projected to be a trilogy, The Lost, Genesis and Identity Crisis. As a whole it is still a WIP, but the first two books The Lost and Genesis are finished. The story has a really interesting premise about Krypton's demise and a lot of original ideas about Krytonite. And it is a true ensemble story with lots of plot and good characterization.
Language of Love, by dogpoet. Slash, Clark/Lex. (ca. 21,200 words)
It's an AU with Clark in college and Lex as English professor teaching poetry. Strangely enough it works, at least if you're not fundamentally opposed to somewhat schmoopy stories.
Futura, by Hope. Gen. (56 K)
Putting Clark and Lex in a Homicide: LOTS setting is not something I would have expected to work, but it does surprisingly well.
The Road Not Taken,
by Joyfulgirl. Het, Slash, Clark/Lex, Chloe/Whitney, Clark/Lana, Lucas/Lana, Whitney/Lana, Lex/other, Clark/other (not all explicit). (ca. 86,200 words)
The premise is "what if Lex had been raised by his mother and Pamela," and it is very convincing, that is the ripple effects changed some things subtly, others quite a lot, in this epic exploration of a slightly twisted SV universe, but everything stays very plausible and in character.
Divergence, by Lanning Cook. Slash, Clark/Lex. (ca. 23,100 words)
Maybe I'm just a sucker for the chance of a happy ending against all odds, but I like how this AU manages to pull off that Clark and Lex can be best friends and lovers and still Lex can become Superman's arch nemesis at the same time. And the way this AU resolves the Gordian knot of a possible future for Clark/Lex is just wacky enough that it's believable in the Smallville universe. The AU started with the vignette Identical (ca. 1,000 words), though the in internal chronology of the series it comes later. By now Divergence has several sequels, so you should just check out the whole Identical series.
Bizzaro World, by Lint. Gen (heading towards Het, Clark/Chloe, though). WIP
The premise is "What if Clark grew up in the Luthor household?" and I like it quite a bit so far (which atm is chapter six). However the author's choice not to put Clark's dialog inside quotes doesn't really work for me, even though it adds a bit to the ambience of the Clark POV. (And the story has some typos, so if you're sensitive towards that, you might be annoyed.)
Just Pie, by Livia.(ca. 2,900 words)
It's really funny, but not a parody. It's kind of wholesome hookerfic, you should just read it... (also on AO3)
Altville, by Livia. Slash, Clark/Lex. WIP
Another story where Lex (here Alexander) grows up with the Kents, and Clark (here Julian) is taken in by the Luthors, yet each take on this popular AU premise is different, and this one is among the best realizations. Not only are Clark and Lex still believable, even though they're different, but I really enjoy the way this story still follows canon, for example with mutant of the week incidents, and is consequent in just changing one thing in the timeline, not all events at random. And I really like how Pete and Chloe and many other characters turn out in this universe.
The Yard, by Jenn. WIP
Clark and Lex somehow (the mechanism how venturing into a yard caused this isn't clear yet) land in a reality where Clark didn't arrive alone. I have a weak spot for all kinds of post-apocalyptic stories, and I certainly want to find out what is going on in the alternate reality, how Clark and Lex got there, and how they might get back. I love how Clark and Lex try to make sense of their situation, and we discover the alternate reality alongside them. More bits are available through the author's associated journal tag, but the collated first part is currently only online through the Wayback Machine link above.
Post-Apocalyptic, by Shrift.
It's a drabble, providing a glimpse into a an alternate reality where Kal-El didn't come alone.
Macellum, by Sylvia. Slash, Clark/Lex. (ca. 19,300 words)
An AU where Lionel takes in the stranded alien (who isn't named Clark by him, obviously) and the family dynamics and byzantine plots, machinations and power games of the Luthors are very convincing, and true to the characters, even to Clark's, who of course is different yet brings his own style to his "Luthorness" so that you can see the canon Clark shine through.