I've always been a fella that tries to find fun in games that are often forgotten or ignored. I find this thread facsinating!! However, I've tried nearly each game listed so far (other than deadite's Thunder Cross 2 and Ken-go recommendations) having read/heard/discovered praise for most mentioned...
With that being said, let me see if I've got a couple underrated games I've found totally unheard of that you guys could check out.
Hook (SNES) I prefer the SNES version of the Genesis or Sega CD versions. I really enjoyed this one with the flying element and the challenge being pretty high in the earlier stages. I didn't necessarily think this licensed game that doesn't suck really brought anything truly new to the table, but I have a blast picking it and playing through it. Kind of felt like one of those Capcom SNES type games with the graphics, music and challenge. Also, enjoyed it's spiritual sequel - Skyblazer also on SNES.
Sonic 3D blast (Only the Saturn version) - I know it's not the Sonic game we all hoped it would be, but I think all the ragging on this better than average isometric platformer needs to stop. It's fun, has clever level design, great boss battles, awesome soundtrack and is a save feature away from being in my top 10 favorite Saturn games. Dang it!
Micro Machines (NES, SNES, N64) all of them. They're hilarious fun that hardly anyone talks about.
Flip Out! Atari Jag You are* - really fun puzzle game that kind of just plays like a quick lunch break, but sucks you in and I often find myself playing through it to the end.... Honestly a little pointless, but a bright spot in an otherwise abysmal game library.
Sonic Spike TG16 - all of you guys that just ignored it and think it's a lame Volleyball game never played 4 players. period. Try it. It's freakin' awesome!
Lagoon (SFC/SNES) port of a x68k game.
That's actually really cool, I didn't realize that Lagoon was ported from anywhere! YAY! Information blast!!