From “Terminus” (paraphrased)
DOCTOR: It'll be good to see the Tardis again.
NYSSA: And Tegan.
DOCTOR: Yes, well, it'll be nice to know she's safe.
[Tegan stands eagerly waiting]
DOCTOR: What are you doing?
TEGAN: I was trying to reach you. Turlough went back to the Tardis on his own.
DOCTOR: I told you not to follow me.
NYSSA: Doctor, say you're pleased to see her.
DOCTOR: Yes, well, I'm pleased to see her but she shouldn't have followed us.
I’m not fond of Nyssa as a character, cause she’s so boring, but I will congratulate her for that.
From "the Five Doctors"
[The Guard Commander has brought a casket, and places it on the table.)
COMMANDER: As you can see, Lord President, the casket bears the Seal of Rassilon.
BORUSA: Where was this found?
COMMANDER: In the Castellan's room.
(Borusa raises the casket' lid to reveal scrolls inside.)
FLAVIA: Black Scrolls of Rassilon!
DOCTOR 5: Interesting. I thought they were out of print. [reaches to pick them up]
BORUSA: Don't touch, Doctor. This is forbidden knowledge from the Dark Tower.
(The scrolls burst into flames so Borusa closes the casket.)
Not strictly applicable in this list, but the Doctor's line amused me and I do hate it when people watch with their hands.
From "the Waters of Mars"
Adelaide: You should have left us there.
The Doctor: Adelaide, I've done this sort of thing before. In small ways, saved some little people. But never someone as important as you. Ooh, I'm good.
Adelaide: Little people? What, like Mia and Yuri? Who decides they're so unimportant? You?
The Doctor: For a long time now, I thought I was just a survivor. No, but I'm not. I'm a winner. That's who I am. The Time Lord Victorious.
Adelaide: And there's no one to stop you.
The Doctor: No.
Adelaide: This is wrong, Doctor. I don't care who you are. The Time Lord Victorious is wrong.
The Doctor: That's for me to decide. Now, you'd better get home. Ooh, it's all locked up. You've been away. Still, that's easy. [opens door with sonic screwdriver] All yours.
Adelaide: Is there nothing you can't do
The Doctor: Not any more.
From "the Vampires of Venice"
Rory: You know what it's dangerous about you? It's not that you make people take risks, it's that you make them want to impress you. You make it so they don't want to let you down. You have no idea how dangerous you make people to themselves when you're around.
From "the God-Complex"
Rory: Every time the Doctor gets pal-y with someone, I have the overwhelming urge to notify their next of kin.
Good old Rory.