From Bulbapedia, the community-driven Pokémon encyclopedia.
A secret card is a card whose collection number is greater than the listed number of cards in the set, for example, numbered 101/100. Secret cards are generally rarer than the other cards in the set, and typically are holofoil cards as well.
The first of the secret cards which appeared was Dark Raichu in the Team Rocket expansion. It was not included even in the Japanese version of the set, as it was made by Wizards itself.
Secret cards seem to be an invention of the English version of the TCG, as all cards released as "secret" have been included in the normal set numbering in Japanese.
Many secret cards are also box toppers.
List of secret cards