Some other possible ideas:
Songstress Yuna and Lenne - Final Fantasy X-2 (girls)
Subaru and Hokuto Sumeragi - Tokyo Babylon/X-1999 (Subaru - boy, Hokuto - girl)
Pallom and Porrum - Final Fantasy IV (again, a boy and a girl)
Dante and Vergil - Devil May Cry 3
Terra and Esper form Terra - Final Fantasy VI (two versions of the same girl)
Hakuryuu and Seiruyuu - RG Veda (boys, and very obscure)
It's all fun and games until someone loses an eye...then it's CLAMP.