Hmmm, have to pick one eh? That's tough. Can't put a finger on a single piece in my collection that I would consider to be the "rarest", especially since a few of them have never been seen in the open market.
I'll just make it easy for myself and share a piece that resonates with me the most as it also happens to be my most favorite game of all time...that would be my Shenmue Limited Edition signed by Yu Suzuki (
not to be confused with the infamous one that sold on eBay).
Shenmue (DC) Limited Edition signed by Yu Suzuki with "What's Shenmue?" Promo Disc

Shenmue/Official Dreamcast Magazine-Shenmue Review Issue/ODM GD-ROMs(complete)
/Shenmue Official Strategy Guide(Prima)/Dreamcast Press Kit

Words can't describe how mind-blowing this game was to me, even to this day. I still remember watching the (epic)
promotional trailer found in ODM's November issue demo disc (pictured) over and over again up to the game's release.