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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.
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? The 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.
The Tenth Doctor vs. the Valeyard.
A grand one for the author himself, in writing a story that not only is considered one of the best Doctor Who fan stories ever, but doing so in a way that doesn't conflict with any of the reveals made during the Eleventh Doctor's run, particularly during the Xof theDoctor arc.