I think Panzer Dragoon Saga is definitely one of the most underrated/hidden gems for the Saturn. My personal favorite game for the saturn is Galactic Attack (aka, Layer Section/Gun Lock/Ray Force in the arcades). I still have my Saturn hooked up just so I can still play this classic shooter.
Astal, though I can't really be sure how well it was received at the time of its initial release (i.e., maybe it was highly rated). I discovered it a few years ago and was blown away by the quality of the graphics and music.
There were a great many arcade ports that were fantastic on the Saturn. Its strength was really as a 2D system. From SHMUPs like Darius Gaiden and Thunder Force V to fighters like X-Men vs. Street Fighter and Samurai Spirits, it was an arcade rat's console.
I think the best game for the Saturn is Dragon Force. I saw the game while I was working for a video game store and had to buy the console and the game. I still play it to this day but had to purchase an external cartridge to save my game play. I had never heard of the game until Saturn became a defunct console.
I did a 7-month cruise on an aircraft carrier and one of the guys in my unit had a Saturn with Crazy Taxi. It got us through! (Well, my Gameboy Color with Shadowgate and Metal Gear also helped). Funny thing was, the magnetic fields are so bad from the arresting wires and gear that the TV we used was always purple and wavy. Good times.
Anyway, that game doesn't really hold up now, going back my memories were a little ruined.
Easily, EASILY, the most underrated SEGA Saturn game is Death Tank Zwei!
It's an amazing hidden game in Duke Nukem 3D, that can be unlocked if you have a copy of another Lobotomy Software game (Quake/PowerSlave) in your Saturn's memory.
Add a Saturn Multitap, 6 additional controllers, and 6 buddies (7-player game) with a lot of extra time, and you'll be playing this far underrated Saturn gem for many hours on end.
We usually pull all-nighters on this excellent little tank fragging game.