I'd have easily said the Borg queen and the supremely stupid Shinzon, but I think something has in my mind more recently edged them out -- and that's no mean feat considering how utterly shit the aforementioned are.
I know, what in the world could edge those out? The the fallic whale probe (probably soon to be banned from the board like the penisrock, since, well, it looks like a giant...).
At first glance it appears to be nothing more than a probe that simply wanted to re-establish contact with one species of whale (fuck all the other whales, right?). But with broader thought, this is an evil villain.
Think about it. A giant probe -- regardless of whether or not you can say how sophisitcated it is or whether or not there was any life on board -- that dampens and harms life on any vessel nearby yet seems oblivious to it, invades areas of inhabited space without announcing itself or it's intentions, heads straight for the heart of Starfleet, causes terrible window-breaking weather, starts draining the planet of the very habitat the species of whale lives in, while desvestating the planet and causing a planetary distress call.
Never mind that the probe doesn't seem to give a fuck about the other whales in the ocean or other species for that matter, it's destroying the place that species of whale lives in. Even if it found one (arguing in this sake that it wasn't extint) and the whale survived, it would be a small condolence to the species; the ecological habitat would be laid waste, the food supply of the species would be laid waste, and the planet would likely not recover from the event, which could cause massive shifts that would end up killing off the whale, including drastic weather dips from blocked out sun. And what about intelligent life? Never mind that fucking stupid comment from Spock about "human arrogence", what about the arrogence of that alien life? Kill everything else in an attempt to contact one species, including the food and home of that species, in order to brielfy re-establish contact?
Probe: "Hey, you still there?"
Whale (translated for you): "Yeah. Holy shit -- you destroyed my home! And I can't find any food!"
Probe: "Great to hear from you. Bye-bye!" leaves.
Further more, who knows how many other inhabited planets this probe has devistated to re-establish contact with a species of whale, or bird, or rat and so forth. It's an intersteller war machine that kills planets to check up on it's pen pal.
No intelligent, well-meaning, caring race would design such a monster.