Ugh...off the top of my head:

Color Variations:
Original Grey
Clear Green
Clear Turquoise
Clear Black
Clear Orange
Clear Purple
Clear Red
TRU Gold
Pokemon Deck and Controller

Package Variations
Atomic Purple Controller
Donkey Kong Jungle Pack
Star Wars Episode 1 Pack
Pokemon Stadium Pack
TRU Gold Version
The one with the Oddball Green Controller (Nuclear or something?)

My brain keeps wanting to add one more in each column, but nothing's coming to mind...