The moment in the final battle where in order to defeat the Dalek conditioning in Ten's mind, all ten Doctors unite to fight it, sharing their memories with one another. This leads to a sequence of MOA quotes from each Doctor, including "First things first, but not in that order", "Just this once, everyone lives", and "That's what kind of man I am." This also counts as a Mythology Gag, a Heartwarming Moment, and a Tear Jerker all rolled into one.
And just a few pages after that, when it seems like the Doctor's psyche is going to fracture, the Dalek conditioning tries to give him a "The Reason You Suck" Speech, and the Doctor responds with a great Shut Up, Hannibal!:
Dalek: You require control, Doctor. It has always been said...how often have you been accused of causing more damage than you repaired, Doctor? How often were they right?
Doctor: Oh, but how many lives have I saved? How many civilisations are free from slavery? Tyranny? I do far more deliberate good than accidental evil. And you only offer disciplined, logical destruction. No, Dalek. I do not accept!
After so many TV episodes with the Doctor going on about all the "harm" he does to those around, him, it's very refreshing.
Three's uses of Venusian Aikido to take out both Cybermen and Daleks.
Leela stabbing the Valeyard, resisting Dalek Ahn's conditioning efforts, and finally racing after the Doctor to try and stop him from killing her Dalek-Time Lord-human children.
