Well I know the MB Red Tracks has already been mentioned, but as an Optimus Prime fan I have to say that the Red Foot Optimus Prime is pretty rare. Red-footed Optimus Prime Also honorable mention to a MISB G1 Canadian Pepsi Prime.
Excluding Lucky Draws of Gold BWII Galvatron or "Crayola Convoy" variety which had so few produced and looking purely at "you actually had a shot at it" release figures, I'd nominate Mass Production Noisemaze, which in retrospect has quite the ironic name. Mass Production Noisemaze was the figure included with the last volume of Galaxy Force on DVD in the figure and DVD set line, which made him available not in toystores, but media stores. As the prior volumes had sold very poorly the number produced was truncated to the smallest run yet; some rumors were under 2000 produced. The entire stock was sold out during the pre-order phase. If you had a pre-order you got the figure, otherwise you were out of luck, whereas the prior volumes figure and disc sets are still available on some of those same sites even with a discount after all this time. Because of that it was also the only set that never made it to shelves as the entire stock was spoken for before the product released.
