Crossover/Fanfic

A-C

 * Ace Combat: The Equestrian War (Ace Combat, My Little Pony Friendship Is Magic)
 * Ace of Spades (Batman The Dark Knight, Harry Potter)
 * Adventures of the Links (The Legend of Zelda and other Nintendo franchises)
 * Aeon Natum Engel (Cthulhu Tech, First Encounter Assault Recon, Neon Genesis Evangelion)
 * Aeon Entelechy Evangelion, the rewrite of above.
 * Affliate Zero (Kamen Rider, Super Sentai and a lot of Tokusatsu-related)
 * Allegiance (Danny Phantom, Harry Potter)
 * Alpha Outpost Blues (Halo, Red vs. Blue)
 * An American Superhero in Japan (comics + Anime, all-original characters)
 * And If That Don't Work (Neon Genesis Evangelion, )
 * And Superboy Makes Three (Young Justice, Marvel)
 * Anti Cliche and Mary Sue Elimination Society (EVERYTHING)
 * Ariana Vampire Queen (Twilight, The Omen, Harry Potter, Glee, The Kite Runner, ''Kung Fu Panda')
 * A Shadow of the Titans (Jackie Chan Adventures, Teen Titans)
 * As Time Diverges the Mitakihara Case (Death Note, Puella Magi Madoka Magica)
 * Ascension (Neon Genesis Evangelion, Half Life)
 * The Assassins Archives Ginevra (Assassin's Creed, The Company Novels)
 * Back to The Frollo (The Hunchback of Notre Dame, Back to The Future)
 * Balto Futureshock (Balto and The Watchers)
 * Basils American Tail (The Great Mouse Detective and An American Tail)
 * The Battle Fantasia Project (Super Robot Wars-style Magical Girl Mega Crossover)
 * Battle Of The Sheps (Ultimate Showdown of Ultimate Destiny with Sheps from Mass Effect, Stargate Atlantis, NCIS, Modern Warfare 2, and Half Life)
 * Better Living Through Science and Ponies (Portal, My Little Pony Friendship Is Magic)
 * Big Human On Campus (Ranma One Half and Rosario+Vampire)
 * Big Sister (Warhammer 40000 and
 * Binky Pie (My Little Pony Friendship Is Magic and Discworld)
 * Blood and Fire (Halo, Mass Effect)
 * Blood That Flows (Magical Girl Lyrical Nanoha and Slayers)
 * The Blue Blur of Termina (Sonic the Hedgehog, The Legend of Zelda)
 * ABLU Haired Medic (Sailor Moon, Team Fortress 2)
 * The Biju Biju Fruit (One Piece, Naruto)
 * Both Syllables (Invader Zim, Buzz Lightyear of Star Command, Lilo and Stitch)
 * Brutal Series (Hunger Games, Hetalia)
 * Calvin At Camp (Calvin and Hobbes, Ed, Edd n Eddy, FoxTrot, Peanuts, and Super Mario Bros)
 * Captain Avatar and The Avateers (Avatar: The Last Airbender, and Captain Planet and The Planeteers)
 * The Captain of the Virtual Console {Many Video Games, a la Captain N}
 * Card Captor Harry (Harry Potter and Cardcaptor Sakura)
 * Chance Encounter (Kingdom of Heaven, The Lord of the Rings, Pirates of the Caribbean, Troy)
 * Cicadas Case of the Endless Dreamer (Higurashi no Naku Koro Ni, Umineko no Naku Koro Ni)
 * Creeping Darkness (Alan Wake, My Little Pony Friendship Is Magic}
 * The Cries of Haruhi Suzumiya (Higurashi no Naku Koro Ni, Haruhi Suzumiya)
 * Christian Humber Reloaded (Several works, such as Bionicle, Sonic the Hedgehog and Final Fantasy)
 * Coccinea (Kamen Rider Dragon Knight, Puella Magi Madoka Magica)
 * Code Total Drama Reality (Code Lyoko, Total Drama Island)
 * Connecting the Dots (Naruto, DCAU)
 * Conquest (Star Wars, Star Trek)

D-F

 * The Dark Lords of Nerima (Sailor Moon, Ranma One Half)
 * A Dark Knight Over Sin City (Batman, Sin City)
 * Dark Titans ( Ranma One Half, Teen Titans)
 * Dead Fantasy (Final Fantasy, Kingdom Hearts, Dead or Alive)
 * Dave Stdider Pokémon Traner (Homestuck, Pokémon, Pirates of the Caribbean, Thor, Digimon, The Legend of Zelda, Naruto, CSI, Twilight, Team Fortress 2, Super Mario Bros, Halo)
 * Demon of Justice (Gundam Wing, Oath Of Swords)
 * Diddy Kong Racing 5000 (Nintendo and Rare Mega Crossover)
 * Digimon Accel Stream (Digimon, Anime, Other Pop Culture References)
 * Digimon Fusion Kai (Digimon, Dragonball)
 * Digimon Fusion Kai Battle Age (Fanfic game based on Kanius' Digimon Fusion Kai, Digimon, Dragonball)
 * Disgaea Gehennas Holy Queen (Disgaea, Mahou Sensei Negima)
 * Disgaea Presence of Hope (Disgaea, Mahou Sensei Negima, with cameos from The Sandman, Soul Nomad and The World Eaters, and other series)
 * Divine Blood (Ranma One Half, Full Metal Panic, Ah My Goddess)
 * The Dresden Fillies (My Little Pony Friendship Is Magic, The Dresden Files)
 * Drunkard's Walk (Valdemar, Bubblegum Crisis, Sailor Moon, Ah My Goddess, Kodomo no Omocha, Buffy the Vampire Slayer, and many more...)
 * Dungeon Keeper Ami (Sailor Moon, Dungeon Keeper)
 * Dust of the Stars (Battlestar Galactica Reimagined, Stargate SG-1)
 * Eagles Fall (Mass Effect, Command and Conquer)
 * The Ed, Edd n Eddy Project (Ed, Edd n Eddy, Ratchet and Clank, Kingdom Hearts)
 * Edventure of the Thousand Year Door (Ed, Edd n Eddy, Paper Mario the Thousand Year Door)
 * The Elements of Harmony and The Savior of Worlds (My Little Pony, My Little Pony Friendship Is Magic)
 * The End of Both Worlds (Magical Project S, MW)
 * An Entry With a Bang (Jack Ryan, Battle Tech)
 * Equal and Opposite Attraction (Mahou Sensei Negima, Magical Girl Lyrical Nanoha)
 * Evangelion Gear (Metal Gear, Neon Genesis Evangelion)
 * Eva Possibilities and Fusion Pandemonium (Neon Genesis Evangelion, Dragonball)
 * Face the Strange (Twilight, Harry Potter, Yu Yu Hakusho, and Sonic the Hedgehog, among others)
 * Falling Stars (Fallout, Lucky Star)
 * Falling Stars (Battle Tech, My Little Pony Friendship Is Magic)
 * Fallout Equestria (Fallout, My Little Pony Friendship Is Magic)
 * Fallout Equestria Project Horizons (same)
 * Fallout Equestria Pink Eyes (once again)
 * Fate Black Reflection (Bleach, Fate Stay Night)
 * Fate Ingens Cor (Harry Potter, Fate Stay Night)
 * Finishing the Fight (Halo, Forgotten Realms)
 * Forcibly United (Black Lagoon, Ranma One Half)
 * Friends of a Solar Empire (My Little Pony Friendship Is Magic, Sins of a Solar Empire)
 * Fuck the Jesus Beam (Tengen Toppa Gurren Lagann, Sonic the Hedgehog, )

G-J

 * Ghost in The Evangelion (Neon Genesis Evangelion, Ghost in The Shell, Serial Experiments Lain)
 * Ghost Story (The Dresden Files, Mass Effect)
 * Glorious Shotgun Princess (Mass Effect, Exalted)
 * God of Death (War Craft, Warhammer40k)
 * Going Native (Battlestar Galactica Reimagined, Star Trek the Next Generation)
 * Grand Tour Series (Ranma One Half, Star Trek, Magical Girl Lyrical Nanoha, Sailor Moon, and many others...)
 * GRIT (Ranma One Half and various other series)
 * Gundam Wing Reaper of the SEED (Mobile Suit Gundam Wing, Mobile Suit Gundam SEED, Sekirei, Fate Stay Night, Mobile Suit Gundam Unicorn and some others depending on author planning...)
 * Gurren Jesus (Gurren Lagann, The Bible)
 * Halloween World (Buffy the Vampire Slayer Mega Crossover)
 * Harbinger (First Encounter Assault Recon, Mass Effect)
 * Harry Potterandthe Invincible Technomage (Harry Potter, Iron Man (Marvel Universe))
 * A Hero (Doctor Who, Puella Magi Madoka Magica)
 * Heir to The Empire (Ranma One Half, Sailor Moon)
 * The Hill of Swords (Fate/stay night, Zero no Tsukaima)
 * Hinata Ends With the Soul Calibur (Love Hina, Soul Caliber, Disgaea, The World Ends With You, Sherlock Holmes, Pokémon)
 * Hunted Tribes (Battlestar Galactica Reimagined, Battle Tech)
 * In Flight (Fate/stay night, Sekirei)
 * The Emiya Clan (Fan remakes/sequels of In Flight, crossing over with a lot more series...)
 * The Interference (Kingdom Hearts, Fullmetal Alchemist, Chrono Trigger, Jak and Daxter)
 * Jigsaw Versus the Punisher (The Punisher, Saw)

K-M

 * Kamen Rider Coronet (Kamen Rider, Pokémon)
 * Kamen Rider OOO the Metals of Ikki Tousen (Kamen Rider, Ikki Tousen)
 * Kingdom Warriors Into the Wild (Kingdom Hearts, Warrior Cats)
 * Kitsune On Campus (Naruto, Mahou Sensei Negima)
 * Knight of Lolicon (Twenty-six different fandoms)
 * Kyon Big Damn Hero (Haruhi Suzumiya, Tvtropes, and Higurashi)
 * Larry Boy and The Little Man of Purpleness (Star Wars and Veggie Tales)
 * The Last Son (Superman/DC Comics, X-Men Evolution/Marvel)
 * The Last Spartan (Halo/Mass Effect)
 * The Legend of Eevee (The Legend of Zelda, Pokémon)
 * The Lost and The Damned (Fallout 3, Warhammer 40000)
 * Lovehammer (Sailor Moon, Warhammer 40000)
 * Lovehammer Inc (Sailor Moon, Warhammer 40000)
 * Love Hina Double Trouble (Love Hina, Kamen Rider, School Days, )
 * Madhouse (Pokémon, Team Fortress 2)
 * The Mad Scientist Wars (Narbonic with a little Girl Genius and whatever else the authors feel like)
 * The Magic of Torchwood (Torchwood, some Doctor Who and Harry Potter)
 * The Man With No Name (Firefly, Doctor Who)
 * The Master of Death (Harry Potter/The Dresden Files)
 * Megamix Tournament (Tournament-styled Mega Crossover)
 * Mighty Morphin Mecha Rangers (Neon Genesis Evangelion, Tengen Toppa Gurren Lagann, The Big O, Zoids, Vision of Escaflowne, Yu-Gi-Oh, Transformers, FLCL, Megas XLR, Code Geass, Call of Duty, Read or Die and more)
 * Mystaras Little Ponies Friendship Is Adventuring (My Little Pony Friendship Is Magic, Mystara)
 * My Little Denarians (My Little Pony Friendship Is Magic, The Dresden Files)

N-P

 * Nanoha Genesis Evangelion (Magical Girl Lyrical Nanoha, Neon Genesis Evangelion)
 * Neon Exodus Evangelion (Neon Genesis Evangelion, many, many more)
 * Neon Genesis Madoka Magica (Neon Genesis Evangelion, Puella Magi Madoka Magica, potential Mega Crossover.)
 * The New Lives Saga (Sailor Moon, Pokémon, Zatch Bell, One Piece, Ranma One Half, Naruto, Fuku Fic)
 * New Look Series (Not quite a crossover, rather a collection of stories from a range of series)
 * Of Gods and Men (Death Note, Harry Potter)
 * On a Clear Day You Can See Forever, (Ranma One Half, Sailor Moon, Ah My Goddess (minor characters only))
 * Once Upon a Shooting Star (Rock Band and Guitar Hero meet Super Mario Bros, Pokémon, Mortal Kombat, Sonic the Hedgehog, Banjo-Kazooie, Tales of Symphonia, Final Fantasy, The Legend of Zelda, and Team Fortress 2)
 * One and Only Son (Code Geass, Gundam 00)
 * The Open Door (Neon Genesis Evangelion, Warhammer 40000-centric Mega Crossover)
 * The Otherworld Anthology (Western Animation Mega Crossover)
 * The Otherworld Series (Anime Mega Crossovers)
 * Paint the Town (The Lord of the Rings, Harry Potter)
 * Percy Meet Dora (Percy Jackson and The Olympians, Dora the Explorer)
 * Phoenix's SSBB Case Files (Ace Attorney, Super Smash Bros)
 * Points of Familiarity (Zero no Tsukaima, Neon Genesis Evangelion)
 * The Pokémon Squad (Pokémon, Ka Blam, Doug, Barney and Friends, The Penguins of Madagascar, Axis Powers Hetalia, Sesame Street, Dora the Explorer, and a whole lot more...)
 * Ponies One Half (My Little Pony Friendship Is Magic, Ranma One Half)
 * Postnuptial Disagreements (Sekirei, Fate Zero, Fate Stay Night)
 * The Prayer Warriors (Percy Jackson and The Olympians, Harry Potter, both are which In Name Only)
 * Prince of Darkness No More (Castlevania, Touhou, as well as some Doom and A Super Mario Thing on the side.)
 * Prinz Von Sommerhoffnung (Captain Ersatz/Not Using the Z Word/Writing Around Trademarks Mai-HiME-centric severe AU Mega Crossover)
 * Protectors of the Plot Continuum
 * Project Arashi (Love Hina, Mahou Sensei Negima, Halo)

Q-S

 * Queen of the Void (Zero no Tsukaima, Magic the Gathering)
 * The Randomverse (DC, Marvel Universe)
 * I'm a Marvel And Im ADC
 * Rainbow in Sunnydale (Buffy, Tom Clancy's Ryanverse)
 * Ranma Club (Ranma One Half, Winx Club)
 * Rebuild of Touhou (Touhou, Neon Genesis Evangelion)
 * Reborn (Kung Fu Panda, The Crow)
 * Reflections Lost On a Dark Road (Ranma One Half, Teen Titans, X-COM)
 * Renegade (Mass Effect, Command and Conquer)
 * Resurrection Verse (Captain America, Iron Man)
 * The Return (Ranma One Half, Sailor Moon)
 * Return to Atlantica (Pokémon, The Little Mermaid, Spyro the Dragon, Spore, Godzilla, Super Mario Bros, Star Fox, Beast Wars, Dinosaur King, Jurassic Park, Monster Hunter... the list keeps going on and on...)
 * Reunions Are a Bitch (Battlestar Galactica Reimagined, Stargate Verse)
 * Ribbon and Stone (Harry Potter,Hime Chan no Ribon)
 * The Road to Cydonia (Ranma One Half,X-COM)
 * Roommates (countless books, films, musicals, series -- too many to list)
 * Roommates (Super Mario Bros, Digimon, Pokémon)
 * Roommates: Gian's First
 * Roommates: These are My Reflections
 * Rosario to Kiva (Kamen Rider, Rosario to Vampire)
 * Scott Pilgrim vs. Snow Flower and The Secret Hall Pass (Durarara, Axis Powers Hetalia, Baccano, Fullmetal Alchemist, Gintama; removed from FFN)
 * The Secret Life of Dolls (Dollfic by Cleolinda Jones, writer of Movies in Fifteen Minutes)
 * Shadow of Zero (Dungeons and Dragons, Zero no Tsukaima)
 * Shinji and the Doctor (Doctor Who / Neon Genesis Evangelion)
 * Shinji and Warhammer 40 K (Neon Genesis Evangelion, Warhammer 40000)
 * Shinobi of the High Seas (Naruto and One Piece)
 * Showa and Vampire (Rosario to Vampire Mega Crossover)
 * Sijo Team Ups (Original character + characters from ANY medium)
 * The Simpsonsvs Arthur (The Simpsons, Arthur (duh))
 * Sinner Blue Darks Misfortune (Soul Nomad and The World Eaters, Blaz Blue)
 * Sleeping With the Girls (Tenchi Muyo, Love Hina, Ah My Goddess, Magical Girl Lyrical Nanoha, Ranma One Half, Those Who Hunt Elves, universe-jumping protagonist so possibly others)
 * Slimer in The Machine (The Real Ghostbusters, Transformers Generation One)
 * Smallville X Evolution (Smallville, X Men Evolution)
 * Snakepit (Stargate SG 1, The Draka)
 * Sonichu (Sonic the Hedgehog, Pokémon)
 * Asperchu, a derivative work satirizing the same
 * SOS Pretty Cure (Haruhi Suzumiya, Pretty Cure)
 * Soul Chess (Fanfic) (Bleach, Code Geass)
 * Sparkgate: Agatha and the Grasp of the Serpent God (Girl Genius, Stargate SG-1)
 * Spongebob 2019 (Select Nickelodeon characters, also including Beavis and Butthead)
 * Star Crossed (Star Wars, Star Trek)
 * Stargate Equestria (Stargate SG-1, My Little Pony Friendship Is Magic)
 * Starlight Series (Starlight, Aftermath (Lilo and Stitch, Star Trek), A Trip To Japan (Lilo and Stitch, Cardcaptor Sakura))
 * Stars Above (Lucky Star, Puella Magi Madoka Magica)
 * The Stepbrother Sitch (Kim Possible, Phineas and Ferb)
 * A Sticky Situation (Digimon Tamers, Star Wars the Clone Wars, Pokémon, Lord of the Rings, Digimon Xros Wars)
 * Sterate Baboogeddon (Nintendo, Catgirls)
 * Suikoden Fantasy (Suikoden III, Final Fantasy VI)
 * Super Network Wars (Mega Crossover)
 * Superman Tenchi the Inhuman Condition (Tenchi Muyo, Superman)
 * Supernatural Taisen (Stargate SG-1, Lyrical Nanoha, Rah Xephon, Godzilla, Hellsing, Ultraman Mebius, Hellboy, Super Robot Wars)
 * Survivability (Bleach, Dong Bang Shin Ki, Super Junior, Big Bang, SHI Nee, B 2 ST, other K Pop characters)
 * Suzumiya Haruhi no Index (Haruhi Suzumiya, To Aru Majutsu no Index)

T-V

 * Takamachi Nanoha of 2814 (Lyrical Nanoha, DCAU, Sailor Moon, Mahou Sensei Negima, Cardcaptor Sakura, Fate/stay night, others)
 * Tales of Bleach Unreal Society ( Bleach, Tales of Symphonia'')
 * Tech Infantry (Old World of Darkness, Starship Troopers)
 * Teh Screaming of the Lambs (The Silence of the Lambs, Arthur, Jurassic Park)
 * The Thessalonica Legacy (My Little Pony Friendship Is Magic, BattleTech)
 * Thinking in Little Green Boxes (Deadpool (Marvel Universe), Harry Potter)
 * A Thin Veneer (Star Trek, Babylon Five)
 * Thomas the Tank Engine And The Daleks (Thomas and Friends, Doctor Who)
 * Thousand Shinji (Neon Genesis Evangelion, Warhammer 40000)
 * Thuum of a Distant Utopia (The Elder Scrolls V Skyrim, Fate Stay Night)
 * Time Lords and Terror (Doctor Who,My Little Pony Friendship Is Magic)
 * Mines of Dragon Mountain, the sequel to the above
 * Tired and Wired, (Band of Brothers, The Pacific, Generation Kill
 * To Kill a Thief (Kamikaze Kaitou Jeanne, Death Note)
 * Top Dog (Mega Crossover, main continuities are Naruto, Harry Potter, and Ranma One Half)
 * Transformers: Frontier (Transformers, Macross Frontier)
 * Transformers Babies (Transformers Generation 1, Muppet Babies).
 * Turnabout Storm (Ace Attorney, My Little Pony Friendship Is Magic)
 * The Turn of Haruhi Suzumiya (Suzumiya Haruhi, Umineko no Naku Koro Ni
 * Ultimate Video Rumble (Fighting Game Mega Crossover)
 * Undocumented Features (The ultimate Mega Crossover world, now in its second decade of continuous production.)
 * Unequally Rational and Emotional (Mahou Sensei Negima, Sayonara Zetsubou Sensei, Mai Hi ME, Batman, others)
 * Unfamiliar (Prototype, Zero no Tsukaima) (Yes, seriously)
 * The Unity Saga (Star Trek, Star Wars)
 * The Unofficial MK vs. SF Saga (Street Fighter, Mortal Kombat)

W-Z

 * When Curiosity Met Insanity (Alice in Wonderland plus other franchises from the Disney Animated Canon)
 * When There Was a Tomorrow (Halo, Mass Effect)
 * When Worlds Collide (Total Drama Island, The Life and Times of Juniper Lee, Sixteen, Family Guy, The Simpsons, Danny Phantom, Courage the Cowardly Dog, Kim Possible, Invader Zim, The Grim Adventures of Billy and Mandy, Samurai Jack, South Park, Ed, Edd n Eddy)
 * When Worlds Collide (Darkwing Duck, Danny Phantom)
 * Where On Earth Spies (Primarily Where's Waldo and Carmen Sandiego. Also advertizing mascots like Erin eSurance and Mayhem.)
 * White Devil of the Moon (Sailor Moon, Magical Girl Lyrical Nanoha)
 * Witchblade Sakura (Naruto, Witchblade)
 * XSGCOM (Stargate, X-COM)
 * Yukari Is Free (Azumanga Daioh, Yotsuba&!, and many others)
 * Yu Yu Gi Digi Moon (Yu Yu Hakusho, Yu-Gi-Oh, Digimon, Sailor Moon)
 * Zero Shock (Bio Shock, Zero no Tsukaima)
 * Zero vs. Kira (Code Geass, Death Note)