Free the Pokemon!
This page seems a bit extremist, and I believe its creator has certain ideas I don't really subscribe to. Nevertheless, it's worth a look.

PETPIKA- People for the Ethical Treatment of Pokemon and Instillment of Kinder Attitudes
This is probably the best pokemon rights site I've found so far.

The Pokemaniac
This is just a blog of someone who fancies himself a vigilante...

Pokémon Liberation Front (West Coast Chapter)
This group is not above using terrorism as a means to achieve their goals. While my group cannot condone such actions, neither can we entirely condemn them. Anyway, we've changed our group's name to distance ourselves from them, but we still feel you should check them out, as they seem to be the only other currently active Pokemon rights group I'm aware of....