Does anyone have recommendations for lesser-known games that are worth putting on the system?
I don't know what is lesser-known to you, but here are some titles that sometimes barely get mentioned:
Arcana
A good beginner 1st person dungeon crawler by HAL (of Kirby fame), with a great soundtrack to boot. Try it out, it has an automap feature, so you'll never get lost. And there are no unfair traps in dungeons like most of these types of games. And the music... oh the music.
Brain Lord
Overhead action-RPG with some nice puzzles. By Enix.
Brawl Bros.
Good beat-em up in the vein of Streets of Rage (Genesis). The sequel, Peace Keepers, is also good. But get the Japanese version (Rushing Beat Shura), because the USA version changed a lot of stuff for the worse.
Dragon View
Very good action-RPG, sequel to the much like-it-or-hate-it Drakkhen.
Firepower 2000
This is pretty much the Jackal (NES) sequel we never got. Although this one plays more like a traditional Shoot'em up.
Hagane
Great ninja action game. This is trully the next gen Ninja Gaiden.
Ignition Factor
Overhead action game. You play as a fireman putting fires out and rescuing people.
Joe and Mac 2
This sequel went with a non-linear Metroid-like structure. It's pretty good.
Nosferatu
Plays a bit like Prince of Persia, but there's more action and it's very moody.
Operation Logic Bomb
Sequel to the Game Boy Fortified Zone. Destroy enemies, open new paths, disarm bombs. If you've played Alien Syndrome, you'll know how this one plays.
Pocky and Rocky 1 & 2
Shoot'em up goodness mixed with action and RPG elements.
Run Saber
Plays just like Strider, although it's very easy.
Shadowrun
One of my favorite "RPGs". Great atmosphere, great music, strange characters. You have to ask questions to people to advance the story. It's a mix of adventure with point-and-click elements.
Super Adventure Island 2
This one they went with a non-linear Metroid-like structure. It's pretty good too.
Super Ninja Boy
Nice RPG from this long-running series (in Japan).
Twisted Tales of Spike Mcfang
Quirky Adventure-RPG starring a Vampire.
Ultimate Fighter
Decent action game with RPG elements from this long-running series (in Japan). Sequel to Flying Warriors for the NES/GB.
Wild Guns
Great arcade lightgun shooter (minus the lightgun).
X-Men Mutant Apolcalypse
Decent action game by Capcom.