The Magnificent Seven
Blackraptor M7 Fanfic
The best one out there, updated frequently and with an outstanding icon system to label which of the many alternate universes the stories are set in (sadly, there are no story summaries, which does make choosing harder); they also label the main characters for each story. Like all of Magnificent 7 fandom, the H/C levels are off the charts -- if everyone gets out without major injury, it was a mistake -- but it's fun for all of that. Look for Sarah B., Sue Bartholemew, Peta Collins and Leigh Richards (angst queens of the universe), Estevana Rey, SassyJ (often a high sugar content, but far too amusing to resist), Tiffiny, and Winter.
Wow, this lady can write. La Corrido Del Coyote is actually too good for words, a fabulously drawn novella that captures all of the Seven, well, magnificently, plus an original character your heart will break for. Then, try All the Reasons Why, fabulous Buck-centric fic. And then there's Candles of the Wicked: ovel-length, poetic, gritty, very well done. And then you can go read everything else.
Derry writes some of the best Ezra (and other) fic out there, both in the Old West (The Wages of Sin) and the ATF (ATF: Angie and A Literary Woman, plus sequels) universes. Also check out her occasional writing partner, The Immortal, for her lovely ATF series, beginning with The Informant.
Magnificent 7 Fanfic Archive
Formerly the largest of the archives, but it's not updated as often now, and finding stories with their new organization can be very tricky. Writing quality varies a little more widely than at Blackraptor, but you'll find stories by some of the same authors. Also try Susan Zell, another author you can read it all. Close Quarters is a terrific JD/Casey story, with Chris as a reluctant chaperone.
ATF Virtual Seasons
Magnificent 7 fandom has produced a truly amazing assortment of alternate universes for the Seven to play in, but the ATF universe was the first, and still the most enduring. You can find most of the stories on Blackraptor, but this page houses the episodes written for a fictitious season. Have fun.