Super-sentient spaceships kilometers wide, made up by forcefields, armed with weapons that overload suns and who think that a picosecond is a long time (sound familiar?), are worried about the presence of the Doctor. In fact, they're thinking that it might be wise to sterilise the entire planet just in case. What does the Doctor do? He goes for tea and biscuits. And sets up his chair in the zero-g environs the ships live in (it can be seen here: http://tardis.wikia.com/wiki/The_Also_People. He talks to them nicely and they decide either that he's not a threat or that even if he is a threat, it's not wise to cross him.
Later in the same book he out thinks a ship, and blows up its higher functions with a small bomb that he kept in his mouth. And whistles "anything you can do, I can do better" all the while.
Damaged Goods contains a scene where a pimp/drug dealer and his vacuous wife encounter the main antagonist. The antagonist is an N-Form wearing a human body: the N-Form is a giant metallic thing with tentacles, and its disguise is horrible. It holds a conversation with the drug dealer about distributing the cocaine that contains its engram (thus making it possible for the N-Form to emerge in the bodies of everyone who consumes it.) The pimp/dealer and his wife are so self-absorbed and dull that they fail to notice that they're dealing with something that clearly isn't human: they're only interested in the score. Even when the conversation is over, and the N-Form TELEPORTS AWAY, they still don't think anything odd about it.
The Dying Days:
The last novel by then publisher Virgin Publishing. It's set up as a "anything can happen" novel that will segue into a "Bernice Summerfield Series" (Benny being the main companion of the Virgin era). So when the Doctor seemingly dies (and is thought of as dead by two people who know about regeneration) you think "crap, he's dead". So when three chapters from the end (about fifty pages) a quiet voice whispers "it ends now" to the villain of the piece your blood goes cold and you cannot say anything but "ohh hell YES". Given that said scene goes on to include the lines "the Daleks call me the Bringer of Darkness", "I'm the champion of life and time" "I make history better" and finally "each word louder then the last "I. Am. The. Doctor" and it was,". The Brigadier who's watching this sheds a tear.
And then the Doctor escapes an exploding starship over London by MacGyvering together a parachute / hot-air balloon out of a couple of bin-bags, a canister of helium, and some curtain rings. While in freefall.