My favorites are:

Shinra and Celty from Durarara!!
Kagome and Inuyasha
Miroku and Sango from Inuyasha
Misaki and Usui from Kaichou Wa Maid Sama
Misaki and Akihiko from Junjou Romantica.


Remember people, Canon.

Otonashi & Yurippe (Angel Beats)
Kashino & Amano (Yumeiro Patissiere)
Abe & Mihashi (Oofuri) (even if it's not a yaoi ;__;)
Jin & Menma (AnoHana)
Senjougahara & Araragi (Bakemonogatari)
Taiga & Ryuuji (ToraDora)

Sousuke and Chidori (Fullmetal Panic)
Inuyasha and Kagome (Inuyasha)
Hei and Yin (Darker than Black)

My favorite canon pairing are Geoff x Bridgette, Alejandro x Heather, Tyler x Lindsey, Duncan x Gwen, Duncan x Country, Harold x Leshawna, Owen x Izzy, Trent x Gwen.