Doomsday has to be in there. The pain of the Doctor and Rose's separation, each of them knowing that their lives would continue in alternate universes, was melodramatic clicheville, but, boy did it make me howl.
In A good man goes to war, I never felt that Amy's trauma, at being kidnapped, incarcerated and then having her baby taken away from her was ever treated as anywhere near significant enough. And, ok, it all worked out and Rory and Amy got to spend time with their daughter who's at least a decade and a half older than them, but that emotion of knowing what that child had to go through must have been excruciating. There's nothing worse as a parent than seeing your child go through trauma and not be able to protect them.
I haven't been able to watch The Angels take Manhattan again since it was transmitted. I will do, but I loved Amy and Rory and wasn't ready to see them go. Like The End of Time Part 2, there were lots of little mini cliffhangers where you kept thinking "is this it?" I'm just gutted they didn't get to incorporate the sequel into the episode.
I also found the last episode of Survival quite hard. It was far from certain that there would be a series the following year and there was a fear that this would be the last Doctor Who ever. I'd only just got really back into it and was devastated at the prospect of no more.
A Christmas Carol was another one that really tugged on the heartstrings. Everyone hates the flying sharks, but it was so sad. Katherine Jenkins' beautiful song stirred up memories of the previous year when the Ood sang David Tennant to his regeneration.
But for me, it has to be The End of Time Part 2. Tennant's regeneration. Again, Rusty went overboard with the emotion, with his trips back to see his former companions. That look on his face when Wilf knocks 4 times. The way he says "I don't want to go", the agony he goes through. It gets me every single time.