Can't speak for the NES and SNES.

Genesis/Mega Drive:

Alien Soldier, Eternal Champions, Marko's Magic Football, Cannon Fodder, Comix Zone, Dragon: The Bruce Lee Story, Mega Lo Mania aka Tyrants: Fight Through Time, and of course, Zero Wing.

PS1: Too many to mention, but here are a few salient ones. They may not all be underrated per se but they are games I generally don't hear too much about.

Jumping Flash 1/2, Fade to Black, X-Com: Enemy Unknown (better on PC but this is still a valid version), Ace Combat 2, Suikoden I & II, Transport Tycoon (Although PC versions are superior again), Vandal Hearts I & II (Much better than FFT imo), Alundra (Alundra > Zelda), Poy Poy 1 & 2, Colony Wars series, and Legend of Legaia.