Eh, I can't think of any specific moments that stand out as scary. I'm not easily frightened. If I were to pick one it would probably be a more conceptual horror than a moment with monsters or something. Rory's 2000 year wait was pretty fucked up, waiting around for so many damned years just protecting a box. That one episode where they were in the hotel looking place and each room had someone's greatest fear, that one was kind of freaky due to driving me to think about what I might find in the room meant for me. I dunno, it's hard to choose but it'd be something along those lines.
Weeping Angels, definitely. They're another of those cerebral horrors that get to me where huge beasts don't do anything for me. The Silence is another one like that, which I would place as the second scariest monster.
Favorite Companion?(I'm including Jack Harkniss and Rory in this category)
Amy Pond. If we're including males in this group, I'd have to say Rose was my second favorite and Rory is my third favorite.
Favorite Episode(Mulit-parters included)
The End of Time, definitely. So many feels.