I'm not talking about Collector's Editions - we all know about Ni no Kuni Wizard's Edition & super rare CE's like the ones for Kingdoms of Amalur, Drakengard 3 or Uncharted 2. But the actual games in those sets are identical to the very common ones sold individually, so it's really the extras that are rare - not the games.
So what games truly rare or at least uncommon yet? These are the ones off the top of my head, and I'd call these more uncommon than rare:
PS3:
Marvel Ultimate Alliance 1&2
Afrika
Cross Edge
360:
Marvel Ultimate Alliance Gold
...maybe Culdcept Saga or Bullet Witch?
I agree, regular standard edition Uncharted 2 is rare. Well, I've not been able to find the one without all the crap over top of the artwork. That does seem to be rare.
As for 360, one that has always been rare due to a short print run is Destroy All Humans (I think it's considered part 3)? Seems like Blue Dragon is an uncommon game. PS3 I'm not sure.
Really, there exists a cheat sheet for this now, you can use VG Chartz to research the lowest sales records and finding out which decent games sold like crap. Takes a bit of the guess work out of it. Taking a glace right now, I can see than Akai Katana, Inversion, Murdered Soul Suspect, Morph X, Fist of The North Star 2, Operation Darkness, EDF 2017, etc, all sold terribly on 360. I take basically any single digit, and especially lower single digit sales record as an indication of uncommon, possibly rare.