I suppose one of my funky NMB boards is probably the rarest... I've never sought boards for their rarity, just for their quality, so I suck at this thread. My Model M is a 42H1292 which isn't that rare, but it did come with some interesting custom keycaps. (It was stored in a closet at work (a hospital) and given up for dead. Taking it apart and putting it back together fixed all the dead keys, etc.
My others are all well known boards around here, MX11900, MX11800, Northgate Omnikey 102, a Rocketfish Bluetooth KB/Mouse, and a pile of rubber domes that I can't bear to trash even though I'll most likely never use them.
So to answer the question... none of them.