Mind you these are genuinely rare, not just valuable. A lot of people seem to confound the words "rare" and "valuable" i've noticed.
PS2
Winback 2
Rule of Rose
Blood Will Tell
.Hack GU trilogy
Arcana Heart
Castle Shikigami 2
Disaster Report
Echo Night Beyond
Eternal Poison
Forever Kingdom
Ghost Hunter
Growlanser Generation Deluxe Edition
Guilty Gear XX Accent Core Plus
Gundam Battle Assault 3
Jurassic Park Operation Genesis
Kuon
Lifeline
Monster Hunter
Monster Rancher 4
MS Saga: New Dawn
Robot Alchemic Drive
Rez
Shining Tears
Stretch Panic
Trapt
Virtual On Marz
Yakuza 2
XBOX
Call of Cthulu
Digimon Rumble Arena 2
Jurassic Park Operation Genesis
Land of the Dead
Outrun 2006
Sniper Elite
Sneakers
Steel Battalion
Steel Battalion Line of Contact
Syberia 2
Xyanide
Samurai Showdown V
I would agree with most of these, because in my days of hunting I've only seen each maybe once, or twice. In some cases not never. However, Rez and Stretch Panic stand out to me as two games that I've seen quite a bit of for whatever reason. I've not once seen Trapt, Blood Will Tell, or Forever Kingdom in person.
It's hard to say, there are probably plenty I've only ever seen once. For PS2 I'd say Tsugunai, because I never found that game in the wild, had to order it. Can't say I've ever seen Dual Hearts in person before either, or Under The Sun. Metal Saga seems like another one.
For Xbox it would be harder for me to add anything, because a lot of the games I've bought, I never saw again in the wild. Conker comes to mind, took me 5 years to ever see another copy after I passed up on one! Maybe Curse: The Eye of Isis, or Dreamfall: The Longest Journey? Also, can't say I've ever seen Stubz The Zombie in person before.