(Original post by Hype en Ecosse)
On top of what Ape's said about the villains not being Moffat's creation (I'll add the clockwork soldiers to his list of villains introduced in a series 4 Moffat episode, they seem to satisfy your 'zomg we're pure evil' criterion), I'll address this view that you're expressing to the villains of series 5 and 6.
-The space whale wasn't a monster. Humans were the monster, and their motivation was highly selfish and unethical by today's standards.
-The vampires wanting to save their race...I assume you mean the creatures in Utopia, in series 4 before Moffat was even in a position of power? I'd call the need to eat a sufficiently good motivation.
-The eye creatures: I assume you mean the Atraxi from the Eleventh Hour, I'll talk about Prisoner Zero, too. Prisoner Zero was willing to put innocent people into comas and steal their identity to prevent himself from being brought to justice for his crime. He's also willing to let the Earth burn; evading justice for your crimes - that's a kind and moral motivation? The Atraxi, to bring justice to Prisoner Zero, are willing to destroy the Earth. Destroying someone because they can't give you what you want is kind and moral? Also, how the **** were they not real?
-Silurians: instead of attempting negotiation, going for an all-out war over land because 'we were there first'. That's kind and moral in your view? I suppose you feel the same way about the Israel/Palestine conflict?
-The Lodger ship: kidnapping and killing lots of people to find a pilot for your ship; that's kind and moral?
-Siren - introduces variation. She's the first villain in series 5 and 6 which has been 'misunderstood' and isn't actually a villain at all; I found this dynamic very interesting.
-Clones? You mean the creatures in the Doctor's dream world? They seemed pretty evil to me. There was no motivation for their killing of people. As for the Dream lord himself, I found that an incredibly interesting insight into the mind of the Doctor, showing another flawed side to our hero.
-Whether the dolls were imaginary or not doesn't take away from the fact that they 'killed' for the sake of killing. Sounds pretty evil to me.
-Again, need to survive I'd say is a perfectly good motivation for the minotaur.
-I don't remember any villainous trees. Might be my memory failing me.