Street Fighter 2 Special Champion Edition and Super Street Fighter 2 were better on the Genesis...because the Genny 6 button pad destroyed the SNES controller. Does that count? The Genny port of SSF2 was actually pretty close to the SNES version in sound and graphics though (and was 40 mbit to the SNES versions 32 mbit).

Samurai Shodown on the Genny was better than the SNES version, the SNES version had fully scaled out sprites (they were tiny) while the Genny had fully scaled in sprites (they were huge, but the Genny didn't have Earthquake).

Aladdin was mentioned already, and Earthworm Jim was also. (Shiny developed both, I don't think Shiny developed the SNES version of Aladdin, which was why the Genesis version was different and superior to the SNES version).