Nightmare Fuel: Ian Chesterton's Stalker with a Crush tendencies towards Susan can be rather creepy, considering that he is an adult teacher and she is a fifteen-year-old girl (or at least the Gallifreyan equivalent of one.) It doesn't help that she seems to be terrified of him.
The Five Doctors - Part 3 has a scene where the illusions of Mike Yates and Liz Shaw merge together into a single being, Two-Face style.It looks surprisingly realistic, and can catch first-time viewers off guard.
Squick: Some of the sex jokes can be this. The music video for the song Never Ever Tell Me is one example where some people felt that they went too far. (Though in fairness, it did have the word "Explicit" in the title, so the viewers should have known what they were in for.)
Oswin Oswald. She really wanted to sleep with the Eleventh Doctor and he was willing to do it, but he abandoned her as soon as he realised that she was a Dalek. She breaks down into tears, and tries to comfort herself by watching some TV. Unfortunately, she picks a very sad episode and starts crying again. Unlike the actual show, her Dalek conversion had no affect on her personality, which makes the Doctor look like a jerk for leaving her, especially as he was laughing at her while running away.
The Tenth Doctor is an even bigger woobie than in canon. Here, he hasn't just lost his home planet and race, but also his money, his home (presumably the TARDIS) and everybody he ever knew. All he wants is to be able to do something with his life. Several viewers actually wanted to donate money to his charity, even though it didn't exist.
Visual Effects of Awesome: Or rather, "Audio effects of awesome." The sound editing in the series is hit-or-miss, but when it is good it really sounds like the characters are actually saying the new lines.
, the Doctor asks if he's a man, to which Clara responds with a "no". One incarnation later...