In no particular order, here are some stand-out soundtracks from the top of my head:
-Bionic Commando
-Brutal Legend
-Castlevania II: Simon's Quest
-Castlevania: Symphony of the Night
-Chrono Trigger
-Donkey Kong Country
-King's Field II (KF III Japan)
-Lords of Thunder
-Mega Man 2
-Mega Man 5
-Metroid Prime
-Ninja Gaiden II: The Dark Sword of Chaos
-Panzer Dragoon Orta
-Sonic the Hedgehog 2
-Street Fighter II