I didn't know about any of these "NR" disks people have brought up in this thread. I personally haven't seen anything that rare. As for standard US releases, here's what I've found to be the rarest (note that some aren't really that valuable)

-Bust-A-Move 3000
-Cubivore
-Evolution Worlds
-NCAA Football 2k3
-Phantasy Star Online games (I was lucky enough to get a CIB copy of PSO 1&2 Plus in pretty good condition for $5 a while back )
-Pokemon Box (only sold at Pokemon Center in New York)
-Top Angler
-Virtua Quest

A bunch of people at other forums will tell you that titles like Skies of Arcadia: Legends and Ikaruga are "rare", but I see them all the time. Uncommon, but not rare.