A game I'd love to see a remake of, would be Golden Sun 1, combined with Golden Sun 2. I know they're not that old, but fresh and crisp re-drawn 2D graphics would do wonders on them. Maybe only add a few more side-quests, and I'm happy. Don't think anything like that is ever gonna happen though.
Another game I'd love to see redone, would be Breath of Fire 2. So sad that the BoF-series has been forgotten for so long now.
Speaking of 3D-RPGs though, Skies of Arcadia would be awesome. It's gotten so rare over the years, I'd just love to see it return. I mean - pirates. In the sky.