I suppose it varies greatly depending on which angle your looking at it.
The idea of data fits best in the anime, when pokemon are traded the trainer keeps the old pokeball with the new pokemon in it. Plus sending them via computer to the professor etc makes it most plausible.
In the games, the environment scenario works, as the pokeball is traded with the pokemon, but the pokemon are stored in the PC, like data.
I like an idea i saw elsewhere, where pokemon are converted into light energy, which is captured inside the Pokeball, which is lined with mirrors, effectively storeing th light until it is opened, where it is converted back, but that's just me :L
