Here are my top 5.
1. Astra Superstars - This one had fantastic animation with the 4 meg cart, and really complex mechanics. Not to mention memorable characters (everything from a stick figure to a vampire to a girl in a Santa outfit). Sunsoft made a ton of really underrated games, and this one is no exception.
2. Groove on Fight: Wacky cartoon inspired characters, one of the best soundtracks of any fighting game, great sprites/animation, and fantastic mechanics. What's not to like?
3. Pretty Fighter X - This one gets written off for the fan service aspect, which I don't deny is ridiculous.
4. Sonic Council - One of the strangest fighters on the Saturn, the mechanics leave a bit to be desired and it can be mashed through, but it has some of the best sprites and animation on the console.
5. Asuka 120% Burning Fest Ltd. - Another girl fighting game, this one isn't quite as impressive in terms of graphics but sports Guilty Gear style (and quality) mechanics.
Of course I didn't mention any of the 3D ones, but I love 2D, sprite based games. I'd be curious to know what some other picks people have are.