My answer to this question is pretty much always the same, Knights of the Old Republic 1 & 2. They hold up really well, but can sometimes have issues running on modern hardware. I think an update and a fresh coat of paint would do wonders.
Other then that, I would love a remaster or full on remake of The Legend of Dragoon. An absolute gem of an RPG that never got the love it deserved. New interest in the game could even lead to it finally getting a sequel or something.
Gustof Wind... Dance!
Hey, a man can dream...
There have been rumors flying around the past few months that a Soul Reaver remaster is already in the works and will be announced some time soon.