I really liked Rinoa/Squall, Steiner/Beatrix, Raine/Laguna. I also thought Tellah and Edward had a great relationship. Always teasing each other. Oh and Fang/Vanille. Not sure if that one counts but it should!

Outside of Final Fantasy, I really liked Hix and Tengaar from Suikoden. Flik and Odessa didn't last long but there was obviously some love there. Anju and Kafei from Majora's Mask.

Relationships I hated? I can't really think of any right off the bat.