2)The room full of dummies is creepy.
3)"There's a room here for everyone, Doctor - even you."
4)The Doctor has a degree in cheese-making?
5)"All I want to do is go home, and be conquered and oppressed - is that so much to ask?"
6)"Don't talk to the clown."
7)Room 11, of course.
8)So, it's "The Curse of Fenric" all over again.
10)"A distant cousin of the Nimon" - yeah, they only see each other at Christmas.
11)A house and a new car? Did they win a game show? All the companions that got nothing when they left will be ticked off.
12)"He's saving us."
Overall: The problem with these stories where the Doctor laments how he places his companions in danger is that you know he's going to go on having companions, because him having someone travel with him is such a fundamental part of the show. Iif he continues to periodically get all mopey about how his companions get into danger, he just looks like a big old hypocrite.
Oh, and as to what was in the Doctor's room?
You know what was in the Doctor's room.
Everyone knows what was in the Doctor's room.