Ships List
Following the example of quite a few people on my F-List, I've been working on a listing of my own ships. I'm by no means done. Every time I sit down I think of something else to add.
Comics (Includes Manga and Web Comics)
Cat Street: Keito/Kouichi
Furuba: Hatori/Touru
Friendly Hostility: Fox/Colin, Derringer/Leslie/Kitty
Hana Yori Dango: Tsukushi/Tsukasa
Haru-Sari: Chi-Min/June
Questionable Content: Faye/Sven
Sayonara Zetsubou Sensei: Itoshiki-sensei/Kafuka
School Rumble: Tenma/Harima
xXxHoLiC: Doumeki/Watanuki
Film
Eastern Promises: Anna/Nikolai
Iron Man: Tony/Pepper
Push: Nick/Cassie
Spirited Away: Chihiro/Haku
Star Trek XI: Kirk/Spock, Spock/McCoy, Kirk/McCoy, Chekov/Anything that moves, Amanda/Sarek
Novel
Abarat: Candy/Christopher Carrion
The Abhorsen Trilogy: Sabriel/Touchstone
Christy: Christy/Dr. McNeil
Harry Potter: Harry/Luna, Snape/Hermione
Howl's Moving Castle: Howl/Sophie
Jane Eyre: Jane/Edward
Mary Reilly: Mary/Dr. Jekyll
The Queen's Thief: Eugenides/Attolia
Poldark Series: Ross/Demelza
Southern Vampire Series: Sookie/Eric
The Thorn Birds: Ralph/Meggie
Tithe: Kay/Roiben
Television (Includes Anime)
30 Rock: Liz/Wesley
Alice: Hatter/Alice
Avatar: The Last Air Bender: Zuko/Katara, Toph/Sokka
Battlestar Galactica: William Adama/Laura Roslin, Kara Thrace/Leoben Conoy
The Big Bang Theory: Sheldon/Penny
Bones: Booth/Brennan
Caprica: Sam Adama/Life, the Universe, and Everything, Sam Adama/Badassery
Doctor Who: Nine/Rose, Jack/Nine, Donna/Being Awesome
Glee: Finn/Rachel, Will/Emma, Santana/Brittany
Heroes: Matt/Mohinder, Sylar/Claire
House: House/Cuddy
How I Met Your Mother: Barney/Robin, Lily/Marshall
Inu Yasha: Inu Yasha/Kagome
Kenshin: Kenshin/Kaoru
Kings: Jack/David
Lost: Juliet/Sawyer
The Marvelous Misadventures of Flapjack: Captain Knuckles/Candywife, Flapjack/Adventure
Modern Family: Cameron/Mitchell
The Office: Dwight/Angela, Jim/Pam, Andy/Oscar
Samurai Champloo: Jin/Mugen
Stargate Atlantis: Rodney/John
Stargate Universe: TJ/Young
Star Trek: TNG: Picard/Q
Star Trek: TOS: Amanda/Sarek
Tin Man: Ambrose/DG, Glitch/DG
Torchwood: Jack/Ianto, Tosh/Owen
True Blood: Sookie/Eric, Jessica/Hoyt
The Venture Brothers: Dr. Venture/Brock, Dean/Triana
Web Series
Doctor Horrible's Sing-a-long Blog: Doctor Horrible/Penny
Dorm Life: Shane/Daniel
The Guild: Codex/Zaboo, Codex/Fawkes
Comics (Includes Manga and Web Comics)
Cat Street: Keito/Kouichi
Furuba: Hatori/Touru
Friendly Hostility: Fox/Colin, Derringer/Leslie/Kitty
Hana Yori Dango: Tsukushi/Tsukasa
Haru-Sari: Chi-Min/June
Questionable Content: Faye/Sven
Sayonara Zetsubou Sensei: Itoshiki-sensei/Kafuka
School Rumble: Tenma/Harima
xXxHoLiC: Doumeki/Watanuki
Film
Eastern Promises: Anna/Nikolai
Iron Man: Tony/Pepper
Push: Nick/Cassie
Spirited Away: Chihiro/Haku
Star Trek XI: Kirk/Spock, Spock/McCoy, Kirk/McCoy, Chekov/Anything that moves, Amanda/Sarek
Novel
Abarat: Candy/Christopher Carrion
The Abhorsen Trilogy: Sabriel/Touchstone
Christy: Christy/Dr. McNeil
Harry Potter: Harry/Luna, Snape/Hermione
Howl's Moving Castle: Howl/Sophie
Jane Eyre: Jane/Edward
Mary Reilly: Mary/Dr. Jekyll
The Queen's Thief: Eugenides/Attolia
Poldark Series: Ross/Demelza
Southern Vampire Series: Sookie/Eric
The Thorn Birds: Ralph/Meggie
Tithe: Kay/Roiben
Television (Includes Anime)
30 Rock: Liz/Wesley
Alice: Hatter/Alice
Avatar: The Last Air Bender: Zuko/Katara, Toph/Sokka
Battlestar Galactica: William Adama/Laura Roslin, Kara Thrace/Leoben Conoy
The Big Bang Theory: Sheldon/Penny
Bones: Booth/Brennan
Caprica: Sam Adama/Life, the Universe, and Everything, Sam Adama/Badassery
Doctor Who: Nine/Rose, Jack/Nine, Donna/Being Awesome
Glee: Finn/Rachel, Will/Emma, Santana/Brittany
Heroes: Matt/Mohinder, Sylar/Claire
House: House/Cuddy
How I Met Your Mother: Barney/Robin, Lily/Marshall
Inu Yasha: Inu Yasha/Kagome
Kenshin: Kenshin/Kaoru
Kings: Jack/David
Lost: Juliet/Sawyer
The Marvelous Misadventures of Flapjack: Captain Knuckles/Candywife, Flapjack/Adventure
Modern Family: Cameron/Mitchell
The Office: Dwight/Angela, Jim/Pam, Andy/Oscar
Samurai Champloo: Jin/Mugen
Stargate Atlantis: Rodney/John
Stargate Universe: TJ/Young
Star Trek: TNG: Picard/Q
Star Trek: TOS: Amanda/Sarek
Tin Man: Ambrose/DG, Glitch/DG
Torchwood: Jack/Ianto, Tosh/Owen
True Blood: Sookie/Eric, Jessica/Hoyt
The Venture Brothers: Dr. Venture/Brock, Dean/Triana
Web Series
Doctor Horrible's Sing-a-long Blog: Doctor Horrible/Penny
Dorm Life: Shane/Daniel
The Guild: Codex/Zaboo, Codex/Fawkes