Symphony of the Night or Sin and Punishment ummm ummmm. Even deciding the best in one gen is hard but I think I will give it to Castlevania so much good stuff in that game, Not many games I get over 200% in and still enjoy it.
Other Notable mentions
N64
StarFox 64
Perfect Dark
Mischif Makers
Goemon
PS1
Tomba 1+2
Strider 2
G-Darius
Ape Escape