Oh goodness - for an emotional basket-case like me, there are a lot. But the real cracker is from "The Waters of Mars" - the first time the Doctor tries to leave Bowie Base One. Water floods the base and you can hear the crew of the base screaming and panicking and the Doctor just keeps walking away.
(Note: I tried to find this clip on YouTube, but I couldn't find anything and my computer decided not to let me upload it myself. But I found this video, which is just as heartwrenching as anything. Spoiler warning for all of Tennant's era - plus there's a short bit from the Paul McGann audio "Neverland" that makes perfect sense in this context).
What makes me just sob is not so much what's happening on screen. What got me the first time I saw this episode is that the Doctor could very well save these people - and he even wants to. But because of fixed points in time and all that guff, he can't. The only thing I could think of what how horribly NOT FAIR this was. Of course, the Doctor turns back and does save Captain Adelaide, Yuri and Mia - but his good intentions backfire in a big way. And I am horrified by the fact that the Doctor is saving them (and I feel terrible for wishing the Doctor could save them. Bad fan! No soup for you!). The realization that the Doctor's gone too far - even though I wanted for him to save someone - will ultimately be what kills him in the end (at least, for the 10th incarnation).