Since the last thread one this is long dead, here's a new one.
Personally I think my rarest cards are:
Error Wartortle Base Set
Raichu and Gyarados Shadowless Base Set
Celebi*, Pikachu*, Gyarados*, Flareon*, Kyogre*
Shining Celebi, Shining Tyranitar, Shining Gyarados, Shining Magikarp
I think that covers the biggest ones...