The one that always stood out for me was Donna's mindwipe. The fear and frustration from the leads, the awareness in myself of what a terrible thing it would be to lose so much of what she gained, hit me hard when I wasn't expecting it.

I think I had a misty eye at River's reveal at Demon's Run, but I think that was a sum of all the stuff that had come before.

Oh, and for what it's worth:

Crying again watching the MS exit on BBC3 now.
it was just utterly perfect farewell

Indeed. It didn't make me cry but ''Time'' is to me the greatest NuWho episode ever. Such a perfect sendoff for Matt Smith.

Thought it was quite beautiful. I was a wreck.What a Doctor.

Good lord, is it nearly a year?!

Gone quick hasn't it.

I know its shocking how fast time is going people are right the older you get time does go faster.

I "went misty eyed" over many of the incidents others have already mentioned, but there's one that's not been mentioned which affected me, because I didn't expect it, and made me realise just how good the revived series was (and still is):

Dalek: The plight of that lone Dalek made me more than just sympathise. It had no choice in how it had been made and it was the last, trapped and alone and perhaps beginning to realise how monstrous Daleks are. And CE's portrayal of the total, almost insane, fear and rage the Doctor has when he first realises what's trapped in the room with him.

I don't think I've cried more than I did when I watched Vincent and the Doctor. When he's looking around at all of his paintings and hearing how loved his paintings are. Oh god. It doesn't just get me in the feels, it beats the living daylights out of all of them. Beautiful.