She's So Halogen
Kathe not only got me started reading Smallville fic, but writing it, damn it! The first of the Lex/Chloe writers, her Would You Like Some Java With Your Snark? is, indeed, snarky and funny and romantic. The Pick-Up is just cool. Her stories almost always center around Chloe, whom she groks very well, but she can handle any other character you throw at her. Let Your Shadow Out is a really interesting future-take on Chloe and Lex -- move Chloe to Gotham, throw in the battle between Lex and Lionel, add a generous dose of Raiders of the Lost Ark, and dive in.
Dyce @ Fanfiction.net
In I Drive the Car she's writing Chlex, and doing it as well as she does everything else, so I'll suck it up. And enjoy it, because Dyce writes with humor and snark and a Chloe who is not a boring pod-person, but a smart, funny, independent young woman. Toss in fast-paced banter with Lex (in his function as Useful Guy), and some strange happenings in the Thompson barn, and you've got Smallville the way it should be. There's also a fabulous sequel, You'd Better Not Go Down to the Woods Today, involving Pete, Clark, dinosaurs, and Tinkerbell.
Snuffleupagus at Fanfiction.net
Sister and Brother should be the most heinously unreadable Mary Sue in the history of fanfic. It's not. What it is, is bitingly funny characterization of a wonderful original character, integrated into Smallville canon through dialogue-only stories that don't need any description or other frills. Lilly is exactly what Lex Luthor's (a.k.a. 'Bumpy') younger sister would be like, and whom we desperately wish he had. Trousers of Time is an excellent AU, swapping Clark and Lex's parentage and following from there. It gets quite slashy, which is why I gave it up, and she'll probably never finish it, but it's excellent.
Viv at Fanfiction.net
Screaming Chloe/Lex shipper over here, so I'm very grateful for fluffy, yet still plotty, fic like Everything in This World, which not only incorporates the whole early Clark/Lana/Chloe thing, but moves past it. Metropolis Confidential is substantially more fluffly, but entertaining.
Chapel of Love
Michael Rosenbaum plays Lex Luthor on "Smallville". Michael Rosenbaum also voices the Flash on "Justice League". Some people can take a coincidence like that and run with it, and we're grateful for them. Join Wendi for the romantic adventures of Wally West and Chloe Sullivan, with cameos by pretty much everyone. (Some tangenital slash implied, in a Lex/Clark/Lois triangle, easily ignorable if you so choose. Although I don't know why you'd want to, since it's utterly hilarious.) Snarky, schmoopy and altogether lovely; the highlight is probably Things Just Keep Getting Better, in which the Fab Five of 'Queer for the Straight Guy' home in on their latest target -- Wally! Wendi strikes again in Sanctuary, a Chloe/Wally West romance set in high school that's a sweet, wonderful look at a relationship between a speedster and an intrepid reporter, and all the heartache that superheros -- and their friends -- have to deal with. I can't find these archives anywhere anymore, so links are to the Wayback Machine; it's worth it.
Lucy Mars at Fanfiction.net
Surprise, Surprise is, amazingly enough, Chlex! Aren't you surprised...? A chance encounter at a Metropolis club sometime in the near future gives Lex and Chloe a friendship both desperately need. Louis is an entertaining original character and the entire story is sweet and slowly romantic. the rest of her stories are alternately fluffy and angsty (sometimes both) and worth the read. I'm not as fond of her The West Wing work; YMMV.
Girl Friday, Chemistry, and Wild Coyote
LJC always puts together gorgeous archives, and these three are no different. Girl Friday is dedicated to Chloe, Chemistry to Chloe/Lex, and Wild Coyote to het pairings of all types. All are entirely worth browsing.
Bats and Other Lonely Heros by Caro
Chloe in Gotham is always an interesting idea -- if you toss in Lex as well, you've got my full attention. Chloe is beautifully characterized in this short fic; Lex is enigmatic and still, thankfully, the guy she knew in Smallville, and Batman and Superman weave through the story without ever making an appearance. Nicely handled subtext tops the whole thing off; thanks to Celli for pointing me at this one.
Siege by Nin
Not the Chlex I usually go for, but a thoughtful Chloe and Lex futurefic that shows Metropolis from ground zero. The insights into Chloe, Lex, and Superman are a lot deeper than the simplicity of the story suggests; the subtext is strong and the characterization perfect. Look here for Part 2 and Part 3
Flying Pigs, Paper Hats, and Pretty Girls All in a Row by paperbkryter
I don't like Lana. I'm uninterested in Lana-fic. I do, however, like Lex. Wearing only his underwear. And handcuffed to Lana. Silly and sweet and appallingly true-to-character for both of the parties involved. You might actually come out of it liking Lana -- the show should write her this well.
The Autumn People by Jenn
A moody, almost dark, Chlex future fic, that starts in a dark alley, and moves languidly and poetically from there. Jenn tells her story without any frills, but delivers all the richness of characterization and language possible; the backstory is integrated flawlessly. A gorgeous gem of an NC-17 fic.