Nintendo Wii Nunchuk
Nintendo Wii gun attachment
Nintendo portable touch-screen system - the DS, obviously. Interesting image.
rotation-sensing cartridge for GBA - used in Yoshi Topsy Turvy, and others I think.
Too much detail on the Wiimote expansion plug
While not strictly a controller, these are interesting:
UV-sensing GBA cartridge, likely used for Konami's Boktai RPG.
The GameBoy Micro
What other interesting controller patents are out there?