Inukami!: Yoko X Keita (yes, Yoko is on top) - It doesn't really matter that their relationship is played for comedy, it's still a genuinely sweet one that rarely dips into the realm of nauseating love confessions, snuggly emotional scenes and the usual "romantic" bs. They like each other... Keita's fighting it, Yoko's not. Yoko's going to win, obviously.
I appreciate the femdom aspects too
Gundam Seed Destiny: Auel X Stellar - No one quite believes me that this one is canon... but from at least one scene that otherwise has no point at all and Auel's constant picking on Stellar, I honestly think he had a thing for her. They would have been the cutest thing if they'd lived long enough without getting their memories wiped to do anything about it. Luckily, a gigantic legion of Gundam Seed doujinshi authors couldn't agree more. I like Shinn/Stellar too... but not half as much as A/S.
Neon Genesis Evangelion: Kaworu X Shinji - Kaworu shut Shinji up for an entire episode. That is a feat worthy of inclusion.