CLAMP Same-Sex couples:
Touya/Yuki
Seishirou/Subaru (Tokyo Babylon/X)
Touru/Saya (from X)
Kamui/Fuuma (from X)
Kizu/Tomoaki (from Suki Dakara Suki)
Kakei/Saiga (from Gohou Drug)
Kazahaya/Rikuo (from Gohou Drug)
Kentarou/Takeshi (from CLAMP School Defenders Duklyon)
Ashura/Yasha (Ashura is technically genderless, true, but isn't Ashura refered to as 'he' in Shurano? )
And lots of other couples, among which I would count KuroFai. Yep, I don't think CLAMP has a problem with same-sex couples. ^_^
And KuroFai is winning slightly! Go KuroFai!