From what I know, they can be used to fight special trainers in Ruby and Sapphire, and can play NES or arcade games by scanning specific cards. It can also be used to unlock southern Island on Ru/Sa via link cable. They can NOT be used in the DS, but do work with the DS lite.
There were also e-reader pokemon cards for a while. Collecting a specific set (ex, clefairy and clefable) would allow you to play a game. Scanning a different code on the card allows you to see a pokedex entry and some strategies for using the pokemon.
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