Landstalker for the Sega Genesis. I have only talked to one other person who has played it. Really, really good Zelda-style action-RPG with a 2.5D isometric view. The box art makes it look pretty generic, which couldn't have helped it commercially.
Speaking of Zelda, both Crystalis and Startropics are two Zelda-style NES games that hardly anyone mentions, and yet I liked them both better than the two NES Zelda games. Crystalis (which had an inferior Gameboy remake) did the whole post-apocalyptic setting before it became too cliche, and Startropics (which has a sequel that I never played) has one of the most unique settings that I have ever seen in a game.
Umjammer Lammy (a Parappa the Rapper spin-off) is another one I enjoyed a lot. Also, Ape Escape. Both for the PS1.