Crono Trigger
It already got re-released with a couple new features on the DS, but if we could get Akira Toriyama and the original team back together for a new version (just don't make it 3D, Blue Dragon makes my face hurt just looking at it) on the PC and new consoles, I'd be ecstatic. The re-release didn't sell incredibly well, so any more work/sequels seem to be out of the question, and this really saddens me. Crono Trigger's excellent story, memorable characters (especially the villains, giant lava porcupines are the best), and parade of silly endings for the completionist in us all left me wanting a lot more. Shame I'll never get it.
One stipulation I'd like to make: if it did get re-released/re-made, don't mess with the turn-based combat. Change whatever else, but leave that combat system alone. These flashier, incredibly bad systems I've seen lately (looking at you FFXIII) are tiresome, often boring, and really detract from my gaming experience more often than not.