So I don't think the Nibblonians are evil and though we're told the Brains are evil, they're really just geeks intent on knowing everything. I suppose in a way, this is 'evil' but I don't know. I think the only thing that made them evil was the disregard they showed all lifeforms as they gathered their knowledge.
Isn't a disregard for all life forms evil, at least in the minds of those life forms? Don't forget, the brains not only want to learn everything. They also want to destroy everything else that thinks. Thinking hurts them, remember?