The Weeping Angels scared the crap out of me in their first appearance and, surprisingly, they continue to do so even now. Steven Moffat truly is a genius of horror/nightmare fuel.
Also the Silents (or is it Silence? I never quite got that) from the new series/season. They totally give me the heebie-jeebies.
I actually found the Ood to be charming, if not outright cute. I always seem happy to see them whenever they pop up in an episode.
And then they get possessed by demons. Every. Damn. Time. I still can't quite bring myself to be scared by them, though.
As for the rest, I always found them either too cool or interesting to really be frightened by them. My curiosity and intrigue overpowered my fears.
Although that psychic space-eel monster from the first episode of series/season 5 was pretty freaky. Those teeth...
And that reminds me, the "vampires" from "Vampires in Venice" were kinda spooky, but the girls were pretty so it was more creepy/off-putting than scary.