The only evil Pokemon are Shaymin and Arceus. It is a well known statistic that in 100% of recorded cases, small, flowery hedgehogs and celestial haloed centuars are pure evil, lords of darkness determined to eat your soul.
Naturally evil Pokemon? None that I can think of. Darkrai, maybe. Its design screams 'evil' to me. Simplistic, really, but as Pokemon as a species are never really explored in any official source I know of. At least not beyond a paragraph of Pokedex text or the anime's simplistically stated morals. I'm not sure about the manga, never having gotten past volume 7, and I don't see any species-wide exploration there, either, which is neccessary to define a species of Pokemon as evil.