Being a hardcore Genesis/Mega Drive addict, I have a few suggestions for hacks. They've probably been mentioned before, but I'll list them anyhow, since this is my first forum post.
Vectorman 2 - Restore the unused options music.
Removing top borders from games from Castlevania, TMNT: Hyperstone Heist, Sparkster, etc.
Minor color improvements for already great games like Toy Story, Stone Protectors (the SNES colors are so much better!), and Mega Bomberman. The Lotus games could use a touch-up or two, but those are just guilty pleasures.
By the way, Pyron's work is awesome!