After looking at a bunch of these posts, I don't think have a single rare item. I don't own a single prototype. Everything I have was officially manufactured and put either in an online store or B&M.
I have Decathalon & Footie for 3DO, Lost & Found 2 + 3 for SS and Pokemon Box US brand new and still sealed for the GameCube. I also have Sonic Adventure LE for US Dreamcast. That's about as rare as it gets for me.
I have plenty of sealed and MINT (I don't own a single game that doesn't look like new) for an array of systems, but I don't think anything is particularly rare or hard to find.