I miss my 3do. Holy crap was it expensive when it came out.
Need for Speed is a great one. Challenging, and the lack of music while driving is actually soothing.
Super Street Fighter Turbo is great with 6-button joystick.
Star Control 2 is the absolute best if you haven't already played it. There's an open source version for the pc called The Ur-Quan Masters that mimics the 3do version well.
Road Rash seconded.
Return Fire too, especially with a friend.
Crash n Burn, a pack in title, was a great deal of fun. I still play this one from time to time via emulation.
Twisted the Game Show is good for a short while. Quirky party type game.
Shockwave is a cool 1 player mission game.
Gex is a solid platformer.