Honestly there are most probably way too many to list all of them here without forgetting a few.
Most of my favorites have already been mentioned.
Here are some random ones that come to my mind:
@nish 's WTB thread introduced me to the WAKA WAKA Exciting Battle set yesterday:
m.bulbapedia.bulbagarden.net/wiki/Everyone%27s_Exciting_Battle_(TCG)
Charizard from the Neo 2 Premium File is also JPN exclusive.
Also many cards with real human photographs weren’t released in English (some of them are in the bulbapedia promo list, but not all):
www.elitefourum.com/t/pokemon-cards-with-real-human-photographs-masterlist-wip/30482/1