I'm stuck between the Angels and the Daleks. The Angels are just plain creepy and have caused me to stare at random angel statues even when they're not weeping. Especially during Mass right after watching "Time of the Angels"/"Flesh and Stone". And the Daleks, of course, are classics. Plus, it's fun to watch them evolve in the series.
I kinda lean towards the Echo and the Burning as being the best villains, actually, in terms of power. No one really understands them, and the Doctor couldn't fight them. They get inside you and then there's nothing you can do. (for reference, everyone who doesn't understand me which is basically everyone who's not me, the 'Echo' is what I call the creature from Midnight, and the 'Burning' is what I call the one from 42). I wish I could find some way to incorporate the words 'Burn with me,' into the Woman in Black item.