I consider Simon's Quest as very under-rated, like E.T. got a bad wrap. I classify it with TMNT as bad games we love, cause they are both are called bad games, but everyone knows of TMNT cause they played it a ton cause most popular game of its time. I think Simon's Quest is like that, minus being uber-popular, but for those of us who loved it, think of it as a gem.
Teenage Mutant Ninja Turtles III: The Manhattan Project
Everybody knows about and has nostalgia for the first two TMNT games on the NES, but most people never played TMNT III: The Manhattan Project since it was a late NES release after gamers had already moved on to the SNES. And that's unfortunate since TMNT III: The Manhattan Project was by far the best TMNT game on the NES and it even gives Turtles in Time a run for it's money as the best TMNT game of all time.
I don't know if it's underrated, but Willow is a pretty great little action RPG. Zelda Link to the Past copied both its sword swipe (which allows you to hit enemies on a diagonal) and its multi-floor dungeons.