I have several "rarer" games in my collection, Varkon (90 made), Starlight (100 made), Joust (402 made), Solar Fire (the 4th of the double level Williams games from 1981 (762 made), Defender(369 made), Time Fantasy (608 made), Algar (349 made), Cosmic Gunfight (1008 made), and a Champagne Fire! (around 300 made) ...They are all pretty popular games in my collection and chances are most of them are not going anywhere anytime soon!
As far as unpopular, I have a Popeye which is IMHO an underrated game, it has many modes and though it has some tough/hidden shots it is a fun game to play. I'm not sure how rare it is, but you don't see them often. It is also not going anywhere except maybe to some upcoming shows!
The only rare 1 that I would love to be able to play and maybe one day own would be Pinball Circus.