I do have a copy of Dune, which is the archetypal rare RPG, but I suspect it is far from the rarest I have. It had a good-sized print run, and I think it’s high price on the used market reflects high demand more than low supply. A lot of self-published RPGs have small print runs, and if they don’t take off they never have a 2nd print run. Sometimes the creator makes the game available in PDF (especially these days), but even as little as 5 years ago that wasn’t a given. So Code of Unaris is basically lost to the world, as are The Shattered Sky, Steeltown, The 23rd Letter, Sketch!, and the Parlor LARPs from Shifting Forest Storyworks.
Then there are games that didn’t even make it that far: I have playtest ashcans of Acts of Evil, Giants, Sign in Stranger, and Kingdom of Nothing, and only the last two have made it to a finished, published version. I don’t know how many copies of each of those were printed, but I know it wasn’t many. For that matter, I have one of the original, numbered copies of Time & Temp, the version as loose parts in a manilla HR folder—I think there were a hundred copies of that?
There are games that weren’t particularly rare when they were new, but that was long enough ago that I don’t hear about them or see them in the wild much any more: NightLife, Bunnies & Burrows, Bullwinkle & Rocky, James Bond 007. And there are games that are still nominally available but largely overlooked: you can buy Great War of Magellan or Albedo from the creators’ websites, but I’ve never seen them in stores,, and they barely get talked about, so I have to think they’re fairly rare in the wild.
But I think my two rarest games are probably HiT: Alpha Limited Edition and Phoenae: the Fierce Joy of Being Alive.
HiT is an attempt to build a scalable game system upon the structure of the Threefold Model. It’s not so much an expression of that model, as the embodiment of a new model that clearly builds upon the Threefold. (For starters, it’s hierarchical rather than multi-axis.) But it’s largely a success as a game system, though the setting/premise are a bit narrow (modern military/mercenary/criminal action), and it never made it to a more polished—or more widely released—version.
Phoenae, meanwhile, is one of those alien fantasy games that defies easy explanation. The characters are cat people, more or less, on a world where that’s the norm. They have either recently awoken to consciousness, or recently lost their memory, collectively, and are trying to learn what it is to be truly alive—to be free-willed. It’s actually a really good premise, and the world is vibrant and interesting, without being overly involved or requiring you to read 200pp just to understand it. Meanwhile, the game mechanics do a really interesting job of trying to give GURPS– or Riddle of Steel-level detail, while working primarily on a verbal rather than mathematical level. That is, the creator tried to make it so that you can say “I parry and then thrust to his left side” and use that directly, rather than first translating each of those actions into a numerical modifier or other mathematical effect. But yet produce the sort of potentially-interesting detail and rigor of a system like The Riddle of Steel. Actually, as I write this, I’m thinking it’s probably even more comparable to the card-based dueling system of Lace & Steel. Regardless, playing a combat reminds me in a good way of Fight! in The Burning Wheel with all the options turned on. I don’t recall right now how well he succeeded at the “hiding the numbers” part of his goal.
Both of these were self-published games that I found at Gen Con, where the creators had a booth. From what I could see, neither sold enough to recoup their costs, and I’ve never seen them in a store. I’ve never even talked with anyone else who has a copy of either, and John Kim needed me to provide a description of Phoenae for his list of obscure RPGs, so I’m pretty comfortable saying they are my rarest games.