I'll second Elly and Fei for best romance. It's terribly tragic but very endearing. Seriously the two wonderful monologues at the start of Disc 2 where Lacan and Sophia talk about their feelings and their drifting relationship is quite touching and feels more real than some of the "I luv yoo!" sap that goes on in other games.

I think my other favorite love story is an odd choice but one that is at the very heart of the game, is Wander and Mono from Shadow of the Colossus. Even the advertisement is summed up as "how far would you go for love?".

Games where you can choose your own relationship never really feel real to me, even in the Persona games which are far more character driven then some Bioware titles, it still always felt artificial to me.