10. The End Of Time 4.17-4.18
While there has been significant backlash against this lengthy story by some who disapprove of the long farewell tour had by the Tenth Doctor in his regeneration story and his comments about regeneration as death, I think it is hard to deny that it opens a door to make regeneration as important to the Doctor on-screen as it is to those in the viewing public and the behind the scenes team. Also, this story also served to reintegrate Gallifrey and the rest of the Time Lords into Modern Who before the Day of the Doctor picked up the ball and ran with it. Atop this, and equally importantly, it started a new chapter in the rivalry between the Doctor and the Master by making them true allies even if only briefly and offered more about the Master's character than we have ever known before.
9. Waters Of Mars 4.16
Doctor Who has done a number of stories on what the consequences of altering time, especially fixed time, are. While it's been handled a number of different and fascinating ways, perhaps the most compelling way the universe says no to the Doctor is its ability to course correct, and therefore subvert the Doctor's attempts to break the rules of fixed time. Waters of Mars has one of the most heartbreaking course corrections we get to see on Doctor Who, as the one person he wanted more anything to save still dies. It is also an important story for the speech that proceeds that pivotal moment. The Doctor by this point has gone absolutely drunk with power. He makes a reference to some of those he has saved, as dismissively "little people" and perhaps worse still, he calls himself "Time Lord Victorious" as the winner of the Time War. It serves a reminder, unlike and above any other, that the Doctor is not naturally good. It is not inherent in being a Time Lord, or a result of his travels. Instead, it's a personal choice he is making and continues to make.