And since I haven't recced in a while, here goes. I'm reccing these by category, rather than by author, although you'll see many of the same authors pop up several times. A few of these are such influential fics, their repercussions are still being felt in fandom.
These are roughly in chronological order. They're slanted heavily towards Jack/Sawyer since that is my favorite Lost pairing. See fics for ratings, warnings and spoilers. Obviously, slash, bondage, death, insanity, and all other manner of dark things.
Lost lends itself well to apocalyptic themes. Here are some of the best I've read:
Three by daygloparker. When everyone else disappears, Jack and Kate struggle to remember them
Two to Go by uberaeryn. Jack and Sawyer must face the end together
Day 365 by maybedarkpink. After a vicious battle with The Others, only Jack and Sun remain
Survivor by eponine119. The first fic I ever read by her, and it's a doozy: by the time Kate is rescued, she's only one of two left on the island.
Red Sky by eponine119. The button doesn't get pushed: is it the end of the world?
The Ruined City by brapolitics. Is it a nightmare or is Sawyer back in the real world, one destroyed by a nuclear war?
This Way Lies Madness
Everyone on Lost seems half-insane most of the time, and then there's the everpresent fear of that mysterious infection.
Paradise Lost by xkatjafx More than a year after it was written, I think this is still the darkest Lost fic ever. Anything dark, disturbing and horrifying can be found here, and yet it's so beautifully written and so extreme, it just takes your breath away. Definitely not for the squeamish.
Schism by themoononastick. Madness and murder among the remaining castaways, with Locke's megalomania in full bloom
Exile - The Fallen by hkath. Only one chapter of what promised to be an ongoing fic, but what's here is still worth reading: Sawyer thinks something is wrong with Sayid.
Wild by alliecat8. Sawyer shows every sign of being infected -- is killing him their only option? (Set after "One of Them.") Part 1 of 3 so far.
Tie Me Up, Tie Me Down
Incest! Torture! And that's the *canon* side of Lost. I could easily do a separate Sawyer/Sayid, Jack/Sawyer kinky/dark!fic rec post, but here are a few that stood out to me:
In the Wild by panthea. Someone is stalking Sawyer. Remarkable for having been written pre-Confidence Man.
Taking a Shot by jaye_voy. One of many "Sawyer gets revenge on Sayid" fics. Runs (or runs over, depending on your POV) that disturbing line between kink and complete cruelty
Taming by eponine119. Based on "The Taming of the Shrew." Jack decides he must tame Sawyer, at any cost. A must-read for any fan of Jack/Sawyer.
In the Dark by cmere. Desmond/Jack non-con. Very creepy.
Fool's Gold by philomel. The darkest take I've ever seen on the Boone/Shannon relationship, as they draw Sawyer into their games.
Multitude of Sins:
Five Things That Never Happened to Charlie Pace by themoononastick. How about prostitution, drug use, torture and character death, for starters? Gets darker as it goes along
Four Hours by cmere. Shannon/Boone, after death. Incest and necrophilia, and yet still somehow tasteful and moving.
Character Death/General Creepiness
The island in Lost is a terrifying place, where anything can and will happen. These are some of my favorite fics on that theme, including variations on "the island is alive."
Nocturna by nekosmuse. Sayid is haunted by strange dreams, and thoughts of Sawyer
The Unknown by literarylemming. An unusual and very unsettling Charlie/Claire ficlet.
Useless Beauty by uberaeryn. Deeply disturbing dreams haunt Jack and Sawyer.
Call It by uberaeryn Another fic about the island trying to destroy Jack and Sawyer in their dreams.
Hunting by kho. A rare fic that demonstrates Walt's strange powers. Excellent Walt/Sawyer interaction.
The Ways by eponine119. Jack contemplates the ways different castaways would choose to die.
Offstage Lines by ficangel. Spooky (and eerily accurate) epic ensemble fic, set between Seasons 1 and 2, in which ghosts walk and talk and the stage is set for a brutal showdown.
A Tale of Gray by foxxcub. A beautiful variation on "Beauty and the Beast." Sawyer finds a mysterious protector on the hostile island.
Variations on the theme that even if the castaways manage to leave the island, the island will never leave them.
Writing Truth by eponine119. Sawyer makes it back to the real world, alone but is haunted by memories of Jack. Maybe more angst than dark!fic but still wonderful.
The Morning After by eponine119. Sawyer comes back to Sydney -- 10 years in the future.
Test Drive by eponine119. Jack is a wreck of a man, until he runs into Sawyer again.
The Disappeared by uberaeryn Even though this is an unfinished WIP, what's there is so damn, shiver-inducingly good. Back in the real world, the remaining survivors are disappearing, one by one.
Normal Again ( Part 1 | Part 2) by uberaeryn. A Jack/Sawyer future fic with sci-fi overtones.
Take the Money and Run by uberaeryn - Jack is still reliving the events on the island that left him maimed (Jack/Sawyer, NC-17, unfinished WIP)
Night on Earth by hkath Jack and Sawyer meet up again on New Year's eve in Times Square, and realize fate is still playing games with them. Not dark so much as mindbendingly cool.
This Act of Searching by thedorkygirl. Barely alive and in constant pain after being rescued, Boone only wants to go back to the island. Interesting for being told from the POV of an original character
Don't see your favorite dark!fic here? Please rec it! ;D Thanks!
And SMOOCH to all these writers for the goosebumps and "OMGZ!" And for making my brain hurt, just a little.