Oooh I totally forgot about Violinist Hameln. That game was fun. It was based on the Violinist Hameln OVA (the series was a lot darker). The game and OVA are just so twisted and wrong.

Deae Tonosama Appare Ichiban. Don't know what it means and don't care. It's similar to Pocky&Rocky. ... To be more precise, it's like Pocky & Rocky meets Cho Aniki. ... Those in the know know and I need not say more.
If you want a cute puzzle game, try out Araiguma Rascal (Rascal The Raccoon). It's a horizontal piece-matching puzzle game loosely inspired by an old anime. And if you are really hip to video gaming, you should recognize the game's theme song (other than that it's from the anime).
If you want to relive the classic game of Qix, you can get Cacoma Knight. It's the same as the classic but with cute graphics.
Clocktower. Not really obscure I guess, but I'll throw it out there.
Go! Go! Ackman series. Based on one of Akira Toriyama's cute manga series by the same name.
Sword World. Based on DnD.
Fushigi No Dungeon 2. Sequel to the game Pokemon Mystery Dungeon was based on. The sequel to FnD2 was on the Playstation, I think.
One of the Great Battle games. Not sure which, maybe it was Great Battle 5. One of those SD Ultraman/Kamen Rider games. It's a bit of a variety pack.
GeGeGe no Kitarou: Fukkatsu! Tenma Daiou. It's just boss fight after boss fight after boss fight. I'm not exaggerating.
Lord Monarch. Ok, so the game sucks. But it was the first Falcom game I ever played and I loved it to death at the time. Played it on my computer. Didn't even know it was on the SNES until years later.
Lost Vikings. Don't think this is obscure, but that's just me. Fun game.
Shounen (or Shonen) Ninja Sasuke. Pretty typical beat'em-up but fun, cute game.
Super Famicom Wars. No reason necessary.