Eiri/Shuichi from Gravitation. And every pairing you can take from the "Mixes" and "Megamixes" that artist made in her doujin circle. Tatsuya/Ryuichi, Ryuichi/Shuichi (which is manga canon), and just a bunch of pairings you wish never existed.
Um, pretty much look up Clamp's works for yaoi and yuri. They aren't yaoi or yuri, but have shonen-ai and shojo-ai undertones that are pretty much canon.
Er...Sora/Riku obviously. Akuroku (ew), Larxene/Namine.
Um...FAKE is a good thing to read and get pairings. Um...what else. Ichigo/Uryu...Ichigo's dad/Uryu's Dad...Byakuya/Ichigo...just put Ichigo with any male and you have a yaoi pairing that is most likely a fan fav.