I used to think that Hatsuharu and Yuki were secretly in love until Rin came along in Fruits Basket. I would probably still support the Haru/Yuki pairing if Rin wasn't so awesome.
My favourite pairings:

Kyou/Tohru (Fruits Basket)
Neji/Tenten (Naruto)
Lelouch/CC (Code Geass) Sorry, but I really hate Shirley.
Ichigo/Rukia (Bleach)
Otonashi/Yuri (Angel Beats)
Matt/Mello (Death Note)

Oh god, where do I start...

Hetalia
Germany/N.Italy
France/England
Canada/Russia
Spain/S.Italy
Sweden/Finland
Canada/Prussia
And a ton of others. I'm not picky with this series.:D

Bleach
Ichigo/Rukia
Grimmjow/Ulquiorra
Szayel/Hanatarou (I swear, I'm the only person who likes this pairing:cry:
Grimmjow/Keigo
Gin/Izuru
Rukia/Orihime
And some others.

Other Random Series
Sasuke/Naruto (Naruto)
Kakashi/Iruka (Naruto)
Zoro/Luffy (One Piece)
Tsume/Toboe (Wolf's Rain)
Ide/Matsuda (Death Note)
Matt/Mello (Death Note)
Mello/Near (Death Note)

I am a fan of KakuzuxHidan, they're just so....can't even find words.
NaruSasuNaru is good too, I can never decide who makes the better seme or uke. I also like Hidan/Deidara...
Oh and the only straight pairing I like in Naruto is DeidaraxIno.

God, all of you edwin or royza fans are CREEPY!

my favorite pairing is obviously EDxROY(fullmetal alchemist) because it's just so adorable.
and of course, next goes WinZa(winryXriza(fullmetal alchemist)). i mean, who doesn't love two sexy women who love each other?

and, cannon pairing is RitsukaXSoubi (loveless)