I love Justin and Feena's relationship in Grandia. It has very smooth development, doesn't feel rushed, and feels completely natural. As they grow into adults from adolescence, so do their feelings for each other. It's tied into their primary character development, but not in, say, a Squall FFVIII way. It's never blatant and overbearing.
Laharl and Flonne because. . .I don't even know, it's not even particularly special or unique. It's cute, though, and made an impact on me.
Tifa's actually a really, really interesting case. She starts out actually hurting Cloud by supporting his lies in Kalm and never quite telling him the truth, stealthily evading it in many cases, until she really must. Her character development is tied into Cloud's; the strange attachment problems ease off and she begins to love Cloud for who he is and not for the fantasy she dreamed and he created. They're definitely incredibly interesting; Tifa gets a lot of attention because of her breasts, but it's her personality and conflicts that makes her one of the better characters in the series.
Celes/Locke is probably my favorite FF pairing.