Since I like both systems this post is in no way a comparison by any means, just wanted to post some of my favorite tracks from both systems.

Snes
Axelay - 06 Colony
Battletoads in Battlemaniacs - Dark Tower
Actraiser - Blood Pool/Casandora
Actraiser 2 - Tortoise Island & Altheria
Contra 3: The Alien Wars - Level 3
Cool Spot - Off Da Wall

Genesis
Battle Mania Daiginjou - Smoking Head
Castlevania Bloodlines - The sinking old sactuary
Phantasy Star 4 - Laughter
Streets of Rage 3 - The Poets II
Eternal Champions - Midknight Stage
Thunder Force IV - Daser Boss