Depends on how you view evilness and how you view pokemon, honestly.
There have been pokemon in-game and in-anime that have done some pretty evil things. Ghost pokemon tend to bother humans and, in recent games, suck out souls and other creepy things, though since it's in the Dex, that could just be folklore. Some pokemon moves seem rather unnecessarily violent, though, like Wring Out >>
And in the anime, there was Mewtwo who wanted to trap trainers on his island and use them to make his own clones, then had all of them fight each other beyond exhaustion. That's pretty "evil" but he also had legit reasons behind his actions and eventually redeemed himself in the end. Unown seem pretty malicious, in both the movie and in the actual show. Legendaries in general tend to be destructive and violent towards each other, which can throw off the balance of the world.
I don't think there are "evil" pokemon, but there can be pokemon with malicious intent, much like humans. And of course, humans can and do influence their pokemon. I believe in an issue of PokeSpe, Red and Blue's pokemon got switched and when they were returned to their original trainers, their behavior had changed from being with different trainers.
