I guess the rarest games I own are near mint condition PAL versions of Earthworm Jim and Earthworm Jim 2 for the MegaDrive
I also have a copy of Star Trek Birth of the Federation for PC, but sadly without the big cardboard box to put it in, so it loses a lot of its value...
I also own a copy of the first-print run Majora's Mask cartridges with the 3D label.
Final Fantasy VII Black Label?
PAL Final Fantasy VI?
*Shrug*
I think there is precisely ONE copy of this game, sealed and signed by Mitsuharu Misawa (the squiggles over the title, and he died about a year after signing it and is also one of the 4 cover guys) as well as Samoa Joe, Curry Man (Christopher Daniels) & Takeshi Morishima.
Not my pic, but I've got one of these:
I have no idea. Skies of Arcadia for Dreamcast maybe?
I also have the Ninja Gaiden Sigma 2 CE, which apparently goes for quite a bit.
Not my pic, but I've got one of these: