My first choice would be Gradius 3. With 1 and 2 already on the platform, it would make sense (definitely more sense than the slow-as-mollasses port on the SNES).
After that, I always liked Magic Sword and the SNES port leaves out a lot of assets and charm of the arcade. With the added space of a Super CD the game could be much less neutered.
Beyond that, the internet rumored Turbo exclusive Mortal Kombat would have been pretty neat. Mostly I'm just curious how well the game would have worked assuming it had 6 button support (and possibly Arcade Card support...)