Amanuensis
'A World Not So Black and White' besides containing one of the hottest sex scene EVER, also paints a realistic evolution of a Harry/Lucius relationship. The saying 'it hurts so good' was created for some of these pieces, particularly 'One Piece of Parchment' and 'A Spell to Turn Tigers into Butter'. Caution: Not for the faint of heart.
Daisy Gamgee
The only piece here is a lengthy novel called History of Us. It's Merry/Pippin, warm, fluffy and sexy. It is the only unfinished piece that I will every recommend because what's already up stands beautifully on it's own.
Dementor Delta
Classic, sleek and witty. From 'Parseltongue-tied' that holds the warning 'Snake Assisted Wanking' to 'An Awfully Odd Adventure' which features a very unusual spin on Peter Pan, her pieces never miss.
Erin
Xena/Hercules, her 'A Funny Thing Happened on the Way to Tartarus' series blows me away every time. And everything else is wonderful too!
Helena Handbasket
The first slash I ever read and I'm still partial. Young Hercules and Smallville fic are particularly good here. Warning: your sides may split.
Icarus
Her Ron leaps from the page and finally takes center stage. The 'Beg Me for It' series makes Ron/Draco fabulous.
Jai
George and Percy written the only way it should be with a taste of awkwardness filled with trepidation and brotherly affection. 'Imperfect' and 'Pressing Matters' hone in on the best parts of Weasleycest.
James Walkswithwind
'Scene Shots', a series of short Wesley/Gunn pieces are succulent and delicate, they paint a complete picture. Anything co-written with Mad Poetess is also a surefire winner, Small Fry and the Domestic Piranhas series are masterworks of comedy and romance.
Josan
What could be better then a Ron/Severus piece that makes me quiver like jelly? While 'Aftermath' is amazing, the real winner here is actully a Snape/OMC piece called 'A Gift of Light'. Severus makes a wonderful father with a wonderful lack of mpreg.
Julad
QaF US' Justin/Brian has never been captured as well in the one page fic "Busy Week on the Fridge".
Mad Poetess
Brilliance. Spike/Xander masterpieces left, right and center. Also, 'Skelping' is a fabulous Doyle/Wesley piece that shows a little ghostly love can go a long way.
Matthew Haldeman-Time
In the newer sections of Buffy fic, there is a wonderful short Xander/Connor piece called 'This Side of the Line" and in the older part of the archive "Are We Friends?" is a marvelous Oz/Graham story that talks about instant attraction, obstacles like werewolf prejudice and a few great jokes along the way. The Jilted Quilted lovers?
Minx
Sirius and Remus have never quite seemed right to me in fic in a post-Azkaban setting. Minx explores this relationship with care and a lot of thought in the Lost Feeling series. If that wasn't enough, it also contains a gorgeous Snape/Harry that makes my knees go weak.
Nortylak
Yes, she made this site and yes, she is one of my favorite people in the whole wide world. She is also, one of the most amazing writers I know. Her Smallville fic is the most notable, definitely capturing the sensibilities of Clex.
Rebop
X-Men only. 'Walking Wounded' is a Jono/Remy that starts with a near double suicide and finds itself in the middle of a great romance.
Rushlight
The brilliant 'Rite of Passage' is a tender Snape/Harry fic that doesn't ere on the side of sap. 'Through a Shattered Mirror' takes you a rollercoaster ride of Harry/Draco/Snape madness that can only be topped off by 'A Fracture of a Mind's Eye', a deeply dark look at Harry's post-war broken mind that will leave you guessing. Her Star Wars: Phantom Menace pieces are the best I have ever read.
Spirit
'The Clockwork Vampire' series based itself on the premise that after getting chipped, Spike ran to Angel rather then Buffy. A simple idea that ran a long, elegant run that also includes the lovely side pairing of Doyle/Wesley.
Sushi
The Civil War verse....defies description. If you have a few days and are dedicated to Snape/Harry this novel will take you through heaven and hell and back. Did I say novel? It is an epic. A wonderful epic.
Thamiris
Her Hercules au fics are a few name changes away from being amazing original pieces. She captures the characters, but makes them wholly her own and comfortable in a variety of historical settings.
Te
I cannot choose just one piece by her. Everything is amazing. But if I must....Buffy- Post-Grad- A Spike/Xander that dates back to when Spike was soulless, unchipped and raw. Also Buffy, Strays an Oz/Xander fic that's filled with werewolf goodness.
Viridian5
Even if you've never seen the Buffy movie or its just been a while, the Pike/Benny Stash series is a great read. A high school realtionship between two outsiders that unfolds into a domestic bliss...of sorts.
Harry Potter
Movie Slash
Multiple Fandoms
Buffy
inner geekdom
Andrew/Xander...so much geek, so little time.
impure things
The Graham/Xanderness of the B:tVS Writer's Guild. It hasn't been updated in a while, but many of the fic there are good ones.
loaded: giles + oz
Great Pairing. Great Archive.
L.O.N.D. Hompage
The Legion of Nerdy Doom. A site for the Troika.
Sidekick Pride
Doyle/Wesley archive. A rarepair with some great contributors.
UCSL: Unconventional Realsionshippers
Possibly the largest Buffy fanfic archive out there.
Harry Potter
Dystopia
Tom Riddle in his many myriad forms. Evil is tasty.
A Family Affair
Weasleycest of all kinds. It's an incestapalooza!
Glasses Reflect: Potter Slash Archive
My start point in the fandom, it contains a multitude of fine fic.
Restricted Section
A NC-17 archive of incredible magnitude.
Perfect?
A bit of Percy slash.
Severus Snape Fuh-Q Fest
Snape, Snape and more Snape. My kind of place.
The Snape/Weasley Archive
Weasley and Snape? Where can one go wrong with that?
Walking the Plank
Harry/Snape classic pieces.
Movie Slash
Bella Donna-Pirates of the Caribbean Slash
Webcrowmaster and L.M. Griffin particularly shine here.
Jay and Silent Bob Slash
Stoners in love.
A Knight's Tale: Slash Archive
You know Wat and Chaucer had something going on....
Satellite of Love
Velvet Goldmine... slash should seem redundant....nope. Still great.
Sith Academy
Over a hundred stories about the days before the movies. Hysterical Hijinks ensue.
Sparrington Archive
Jack. Norrington. Feel the love.
Multiple Fandoms
Bad Fanfic! No Biscuit!
Several Authors teach us the lessons of the truly bad fic.
Complete Kingdom of Slash
This archive has been around for a long time, in one form of another, but most recently was reworked and some of the older pieces weren't restored. Still worth a look though.
The Slash Database
If the fandom exists, it can be found here. The things I have located with this site blow my mind. Check out Minotaur's Guide to Sex for Slash Writers as well.
Polyamorous Recommendations
Not strictly an archive, this rec page spans all my favorite fandoms and then some, turning up gem after gem.