I'd love to see a new Project Eden. The game had some great puzzles, but the fights were rather dull. A new Lost Vikings would be nice too. I like Trine and all, but I prefer having to get all three character to reach their destinations individually instead of them teleporting into each others' place, and the ones you're not using at the moment floating in limbo.
Septerra Core deserves another chance too. It was a really unique cyberpunk "jrpg" hampered by bad voice acting and occasionally tedious quests and grinding. Same with Revenant, it was such a cool Diablo clone with fighting game elements, but some of the dungeons were waaaay too long and maze-like.
Finally, I think Jazz Jackrabbit is ripe for a revival and a return to norm after the atrocious GBA game. Oh, and what I wouldn't give for a good MDK 3!