NES: One has red buttons and one has yellow buttons
SNES: They're both the normal gray ones
N64: Two silver, one purple (you can see through it), and one blue (which you can also see through)
GCN: Two black, and a wireless one that is silver (and I don't think it's an official Nintendo controller)
Wii: Three white remotes, two white nunchucks
EDIT: Playstation: One silver controller (I don't play Playstation very often)
N64: Green, Blue, Grey, and Yellow
GCN: Two blacks, two purples, one orange, and two (new) whites. I wanted to get a platinum one, but it costs twice the amount of one white controller, so I got two white controllers.
Wii: I used to have three whites, but I dunno where the third one is, right now.
1: Wii: 4 white, but two are rechargable; the other two use batteries.
2: PS2: 2 custom Black wireless controllers built by some company called Pelican. They feel better in your hands (or mine) than the standards.
3: Gamecube: One (yes, one) white controller with "Gamestop" stamped across it. Like the PS2 controller, this is custom: it contains a "turbo" button
To also count handhelds:
Transparent GBC (sold; big mistake).
Blue GBA SP.
Grey DS (broken).
Black DS Lite.
Pink DS Lite.
Grey DS (Capture Device).
Black iPod Touch (was jailbroken, and almost about to sell for iPad 2).
Grey Nexus One (rooted and runs custom ROM).
2x Black 3DS (one of them will turn into a Capture Device soon).