I would have to go with the Genesis on this one. Contra III and Castlevania IV are outstanding games, and a must-have in a SNES library, but Hard Corps and Bloodlines are far more fun and show much more creativity. As for the TMNT games, I like them both the same.
Contra: Hard Corps and Castlevania: Bloodlines are my favourite games in their respective series, and despite the inferior graphics and sound processor, I much prefer the visual style and effects along with the music in both games, not to mention they're more fun (IMHO).