Right now this is the fic master list, so read on to see if there's any that interest you. Each individual fic is bolded for ease of reading. Please comment on the one's you like the sound of.
Multi-chaptered fics to finish:
Cause I See You Lying Next To Me: Oli Sykes/Tom Sykes (+1) - Tom gets Oli a pretty boy as a present (porn, last part)
Deaf And Dumb: Frankie Iero/Pete Wentz (with others) - Pete uses Frankie more.. .but this time he's not alone... porn.
My Body Is Your Body: Ryan Ross/Spencer Smith - What's in the box? Porn
Pet: Padge/Ray Toro, maybe others - Ray's taught how to be obedient an made into Padge's 'perfect' sex toy [Unexpectantly got lots of votes, so has been moved up. First part may get rewritten]
The Disadvantages Of Being A Sheikah: Sheik/Twilight Princess!Link eventually, Sheik/Shad - Sheik's entry to the Twilight Realm isn't as random as it appears...
The Hunt: Brendon Urie/Ian Watkins/Matt Tuck/Tom Delonge - In Cardiff at last, Brendon goes on his own to find drugs and ends up finding Ian. Vampirism, porn
The Time Of Our Lives: Bob Bryar/Frankie Iero/Gerard Way/Mikey Way/Ray Toro - Kinky group sex
Tie Me To A Chair - Danny Hall/Dave Williams, others - The final part (when it's done) porn.
What To Do With The Dead: Mikey Way/Ryan Ross (current part, Ian Watkins/Mikey Way for a lot of parts, with various Mikey pairings as well): Mikey tortures and kills Ryan, then mounts his head.
5 Dreams: Various MCR - Based on Buffy Episode Restless, 5 parts long, each with different pairings, though Waycest is prevailent. Each part is a different member's POV/dream
Breathless: Matt Tuck/wiL Francis - Porn at Kerrang XXV, started last year but never finished
Hard Slammin': Dave Williams/Ian Watkins/Matt Tuck/Sean Smith - Porn. Kink, foursome porn. (Fulfilling Lust for Dave's 7 deadly sins)
Mama: Gerard Way/Mikey Way/Omar Abidi - Porn, again. With Mikey (possibly Gerard too) referring to Omar as his Mama. With male lactation. (for smut_69)
Markers: Gerard Way/Mikey Way - Mikey on why Gerard always has something written on him. Smut?
Piggy: Mikey Way/Overweight!Gerard Way - Gerard puts on weight after a guy's dumped him, then Mikey ties him up and rapes him. Mikey makes a point that no one else will have him and that Gerard is his. Kinky smut based on dream
The Gods Want Something: Bob Bryar/Dougie Poynter/Frankie Iero/Gerard Way/Mikey Way/Ray Toro - The ritual scarifice fic I keep mentioning. Cannibalism, rituals, organ removal, necrophilia.
Today We Learn About Oral: Ian Watkins/Ilan Rubin - Take a wild guess on what hapens. Sequel to Hand Work
Where the Wild Roses Grow: Mikey Way/Undecided - Based on the song. (possible smut_69)
Untitled: Benji Madden/Bert Mccracken - Benji admires Bert, sex ensues. Porn
Untitled: Benji Madden/Ian Watkins/Joel Madden - Porn
Untitled: Bob Bryar/Frankie Iero/Gerard Way/Mikey Way/Ray Toro - The surgery fic I keep mentioning, however they'll be two. In this one Ray and Bob decide that Gerard should pay the price for his infidelities to Mikey and decide to ensure it won't happen again. Gore
Untitled: Bob Bryar/Frankie Iero/Gerard Way/Mikey Way/Ray Toro - The other surgery fic, however this one will more closely follow the dream it's based-on. Gerard will be cut open, with his organs exposed and removed. Gore
Untitled: Charlie Simpson/Ian Watkins - Porn (from 50kinkyways)
Untitled: Charlie Simpson/Dan Haigh/Omar Abidi - Both omar and Dan lust over Charlie, so they decide to act on it togeteher(50kinkyways)
Untitled: Dark!Link/Link - Dark!Link bests Link in combat and fucks his corpse.
Untitled: Ian Watkins/Lee Gaze/Matt Tuck (possibly with Jay too) - Ian decides to have a 'bonding session' with his cousin. Porn, kink.
Untitled: Ian Watkins/Oli Sykes (Maybe Sean/Ilan?) - Set on Lostprophets last tour. Porn
Untitled: Jared Leto/Jay James - Jared fucks and fists Jay... all for his brother. Smut.
Untitled: Jared Leto/Travis Barker - Jared has a drummer fetish. Porn
Untitled: Jay James/Matt Tuck - Jay decides to explore Matt's fetish. Scat, porn, kink
Untitled: Jay James/Matt Tuck/Moose/Padge - Based on a short thing with Jay. When Jay gets his cock trapped in a zipper the boys try everything to get him hard again. Porn
Untitled: Link/Ganon, others - Link is tortured and eventually becomes the Prince of Twilight, with Ganon as his master and Ralis as his pet
Untitled: Link/Morpha - Tentacle porn.
Untitled: Link/Ralis - After Ralis says he'll do anything for Link, he takes advantage
untitled: Link/ReDead - Reanimated corpse porn
Untitled: Link/Shad - Drunken sex
Untitled: Miyavi/Undecided - Death by hammer. Porn, gore.
Untitled: Sheik/Gibdo - Undead bandage porn
Untitled: Bob Bryar/Gerard Way - For one night Bob gets what he wants. Porn
Untitled: Bob Bryar/Gerard Way/Mikey Way - 'The idea of seeing you two fucking turns me on.' Porn
Untitled: Bob Bryar/Harry Judd - Sequelish to Bitch. Bob has fun with his new boy. Porn, semi-gore
Untitled: Frankie Iero/Gerard Way, Gerard Way/Mikey Way - Frankie's jealous that his boyfriend spends more time inside his brother then servicing his cock, so decides to take action. Porn, gore.
Untitled: Frankie Iero/Others - Highschool rape. Porn
Untitled: Gerard Way/Mikey Way/Frankie Iero - Companion fic/prequel to Dead! Gore
Untitled: Gerard Way/Tom Delonge - Bob watches as they have sex, wishing he was Tom. Porn, kink.
Untitled: Mikey Way/Gerard Way/Mikey Way - Yep, you read that right. Porn
Untitled: Mikey Way/Madden Twins, Mikey Way/Gerard Way - The twins see Mikey and they want him to be theirs. Gory porn
Untitled: Mikey Way/Pennie - Sequel to Fluffy, porn
Untitled: Mikey Way/Girl!Mikey Way - Mikey hoped to find a guy that looked like him to make a porn for his big brother, instead he found something unexpected. het porn
Untitled: Mikey Way/Various - Mikey has a slight chub fetish...
Untitled: Mikey Way/Undecided - Mikey has no limbs. Porn, gore-references
Untitled: Padge/Frankie Iero - Rough, drunken sex
Untitled: Ray Toro/Ilan Rubin (maybe Ian) - Porn
There's some other smut_69 ones, however, most are just little undeveloped ideas (including one with Spencer chained up and Ray being a slut).