Some of the "Hidden Gems" that I've enjoyed are...
* Kid Icarus: Of Myth & Monsters (GBY) -- Considered the "lost sequel" of the series (most only know the NES game)
* Revenge of the Gator (GBY)
* River City Ransom / EX (NES / GBA) -- A "Cult Classic" that got a remake on the GBA.
* Stinger (NES) -- Part of the Twinbee series, which never got a great footing in the US.
* Trog (NES)
* Vegas Dream (NES) -- While the casino gaming is a bit pedestrian, the random encounters made it interesting.
* EVO: Search for Eden (SNES) -- Hard RPG with an interesting evolutionary mechanic (& related storyline).
* Legend of the Mystical Ninja (SNES) -- First game of the "Gaemon series" that made it to the US.
* Stunt Race FX (SNES) -- One of the few games that used the FX chip for 3D graphics (albeit highly polygonal)
* Earthbound (SNES) -- Cult Classic that's gotten a revival in recent years with VC releases on the Wii U & N3DS
* Gauntlet Legends (N64)
* Rampage (NES) / World Tour (N64)
Most of these games are probably "known" by others but still relatively obscure for most.