The “Pikachu Illustrator” cards have sold for the highest amount, publicly at least. These cards were awarded to winners of a Pokemon contest held in Japan circa 1998. Less than 40 of these cards are known to exist. In recent years, a few have sold for between $100,000 and $375,000.
Gem mint 10 (aka perfect condition) first edition holographic Charizards from the 1999 base set are nearly as valuable. They have sold for as much as $369,000 at auction. Most recently, the card sold for $270,600, according to the PSA.