I find most game romances to be terribly done.

It's not so bad in games like Persona, however, where you build it up the course of the game spending time with the girl you woo. So I'll say Main/Yukiko in Persona 4. Mostly I just love Yukiko, favorite character in the series. <3

Rune Factory 3 also has a goofy charm to it with the Mermaid chick, I forget her name saddly.

For games you don't pursue the romance yourself, FF IX was probably the best done in any Final Fantasy game, and while I do like both characters it wasn't that well done.