The price is not always a good indicator (look at Radiant Silvergun on SS).

For me, among commercialized games :
Fuu-un Gokuu Ninden (plateform)
rockman battle & chase (kart)

it's because I never managed to come up with. that's why rarity is a bit elusive as concept: it depends of many factors; anyway, more than the initial number of printed copies.