For the PS2, Rez is hard to find (I've been looking for a copy forever) and I've heard that Disgaea: Hour of Darkness, Guitaroo Man, and Mr. Mosquito are hard to find, but I have Disgaea and Mr. Mosquito (and it wasn't too hard to get them) and I've seen Guitaroo Man a bunch of times at Gamestop and EB. One game that you will never see outside of Ebay is World of Outlaws: Sprint Cars 2002. If you pay less than $50 for it, go buy a lottery ticket because you have some heaping portions of ethereal assistance guiding your life.
Marvel vs Capcom 2 for PS2 is rare. I picked up a copy with no manual for $15 at a pawn shop. Ebay tends to hold strong to about $80 for that game with no manual.
I found Rez and MvC2 on complete flukes at Gamestops. Rez had a $50 used tag, and MvC2 had an $80 used tag.