...I look at my game collection and answer with "good question".
I'm gonna assume that the answer is Metroid Prime Trilogy or Xenoblade Chronicles, as evidenced by the stupid prices demanded by Gamestop for "used" copies. I actually got my local store's very last copy at the time.
I have a large amount of limited editions, but I doubt those count. My copy of Hyperdimension Neptunia was rare until NISA decided to reprint them at a low cost.
Funnily enough, I didn't really like any of the three games I've mentioned. Metroid Prime didn't grip me enough and was dropped at the first save point, Xenoblade felt merely "okay" and was stopped fairly early, and the first Neptunia is the worst game of its series by far.
EDIT: I also have one of the few physical copies of Code of Princess. Seriously, the print run on that game was so small that most stores only got pre-order copies. Mine only had *one* aside from mine.
edited 26th Nov '13 11:18:55 PM by burnpsy