It's all right for you, Peri. You've only got one life. You'll age here in the TARDIS and then die. But me, I shall go on regenerating until all my lives are spent.
S22 E2Vengeance on Varos
The Doctor [after both of the guards have fallen into an acid bath] (turns to glance back) You'll forgive me if I don't join you.
[walking away after finishing a conversation with and being accused of intolerance by Peri] Intolerant. Intolerant? INTOLERANT!!, ME?!!
[speaking to Quillam] Oh, I thought you were my mirror image — Until I realised I wasn't the one holding a gun.
[speaking to Peri] I think he needs more than water, Peri, eh?
S22 E3The Mark of the Rani
Do you mean the TARDIS is malfunctioning again?
Malfunctioning? [pause] Malfunctioning? MALFUNCTIONING!? After all the work I've done on it!?
Well, I only asked a simple question!
Indeed you did, and it was the wrong question!
What's he up to now? It'll be something devious and overcomplicated. He'd get dizzy if he tried to walk in a straight line.
[After hearing the Master's scheme] ... You're unbalanced. No wonder the Doctor always outwits you.
Guns can seriously damage your health, you know!
'Will you come into my parlour, said the spider to the fly.' [pauses] I think not. Doesn't feel right.
[Referring to the TARDIS]
RRavensworth
What precisely do you do in there?
Argue, mainly.
S22 E4The Two Doctors
[throws a stone into the lake the Doctor is fishing from]
DON'T DO THAT!! You'll frighten the fish!
What's the use of a good quotation if you can't change it?
Perhaps you should see a doctor.
The Doctor [annoyed]: Are you trying to be funny?
Small though it is, the human brain can be quite effective when used properly.
These quotes come from Wikiquote's Doctor Who pages and are available under the Creative Commons Attribution-ShareAlike License.