I bought Thomas Was Alone after reading Critical Miss last Friday. Since then I've played though most of the game, enough to say that the romance between Chris and Laura was really good, especially for being between a cube and a rectangle. Laura shares Chris' weakness (He can't jump very high), and offsets it with her bouncing ability. They complement each other both in personality and functionality.
A lot of people have already mentioned Junpei and Chidori from P3, and I definitely agree. When he falls in love with Chidori, Junpei realizes that up until that point, he didn't really have much of a reason to live. She gives him that and, while Junpei doesn't realize it, he does the same for her.
I also really liked the romances in Odin Sphere, though I've yet to finish that game because it's harrrrd. I'll admit that Gwendolyn is basically sold to Oswald to begin with, but that's more a testament to how much of a monster her father is. Oswald doesn't want to force her into anything, because he genuinely loves her, and when Gwendolyn realizes that, and that he's the first person love her unconditionally, she risks her life to save him.