Shantae Risky's Revenge and the Mighty series (Mighty Flip Champ, Mighty Milkyway, Mighty Switchforce) are really fun games by developer Wayforward.
The ports of Vvvvvv and Cave Story are both great.
Pushmo is a really cool puzzle game with nice 3D effects.
Zen Pinball is an ok pinball game.
And to end, I am a big fan of 3D Classics Twinbee, a vertical shooter by Konami that was on the Famicom.