Well, this is easy enough. Well, since I watched Blink, Weeping Angels are HANDS DOWN the scariest enemy on the show. They terrify me. What's the scariest enemy for YOU? (If I left something out, just say so )

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Are you talking about re-occurring enemies only or ones that might have only been in one or a few episodes? I think the nanobots that turned people into gas mask wearing crazies asking "Are you my mummy?" was pretty creepy. Though I do agree that the Weeping Angels were probably the most scary.

Also, I think The Master should have a spot. He was scary in a maniacal way.

rcarter2 : Oh, I remember that, that scared that crap out of my brother. I'll add those right away sir. 

OMG, the Master is my favorite Doctor Who villain ever! I love him so much! I don't think he's really the scariest to me though...
A lot of people think the Weeping Angels are the scariest, but although they are creepy, I don't think they're the worst. They send you back in time, and its horrible what they do, separating you from your family and all, but at least you still get to live your life, and say goodbye, at least, if you're clever, and make the best of a bad situation. Most Doctor Who villains just don't give you that luxury, although its super creepy how they move when you aren't looking!
I personally would say the Silence are the scariest, or perhaps the Vashta Nerada. The Waters of Mars had some terrifying visuals, though, and that copycat thing on Midnight was creepy. (Colin Morgan was Jethro, though, so I was almost too busy fangirling to notice.) I guess sometimes the shorter lived villains scare me more; I don't know why, although the Silence do show up quite a few times. I guess most reoccurring villains excite me too much, like, "OOH! YAY! THEY'RE BACK!" (I like villains a lot, for some reason.) ANYWAY, ahem, the Silence are pretty creepy, I think, simply because you CAN'T EVEN REMEMBER THEM! How creepy is that?! I guess it's pretty typical for me to fear a thing you can't know anything about, because I hate not knowing things I feel are important. That's just terrifying! The Vashta Nerada really get me though, I think, because for a long time when I was little I was very scared of the dark, and that episode just brings all of that back with its stupid shadows even the Doctor was unable to save people from once they'd attached themselves. Also, I usually have two shadows in my own room, so that nearly gave me a heart attack when I "counted the shadows" while watching that episode. (Two light sources... Ugh!)
Out of the options you had, I'd have to go with the Cybermen. It is SO creepy that they were originally humans, and the whole "upgrading" thing is really gruesome. It'd be terrible to become one of those things, and I think I'd rather die than be something like that. I know the Daleks kicked the Cybermen's butts, but the Daleks are somehow really funny to me, don't ask me why. I just love the Daleks! (In the way that I love villains.) They are so cool!
Awesome question!

I really can't decide between the Silence and the Weeping Angels. It's just not possible. I guess the Silence could be scarier as they kill you in the moment whereas the Angels just put you back in time which isn't that bad compared to death, but I still can't decide.

The silence are creepy. Not so much the appearance or anything but what they do. They will scare you, and put danger on you and the world around yet when they are not present you cant remember or describe them.  This keeps them very secretive and they avoid any sort of hero that can fight them off. A monster that quite literally messes with your head.

Until the Weeping Angels, had to be the 'Are you my Mummy?' nanobots.  Mind you the Auton's (Nestine)  are also quite scary.  Shop dummies coming to life!