Because of the thread title I'm going to make a comprehensive list to resort to whenever this topic comes up again in the future.
In the demo I had to fight back tears as the Reapers shot down the kid's shuttle.
In the full game I didn't get affected by that scene because I realised how creepy that vent scene was. It's either creepy or the kid is extremely dumb and/or sufferes from emotional detachment.
Other instances through-out the game.
Mordin's death. Really really bad. And even on my 3rd playthrough I still shed a tear or five lol. It's a fantastic scene and def in the top 3 emotionally moving moments of the game. HE had a hero's death.
Grunt's scene. When he said "The shuttle's down that path. I'll hold them off. Get out of here Shepard!" and that music started playing I was like "No... No! He can't die!" and then when he came back covered in Rachni blood and asking for something to eat I was smiling with such joy! And immediately thought "What a Krogan."
Liara's Project. Just everything about it was so moving, it was in that scene i reflected the most on where my Shepard had come from in ME1 to where she was right then. A great scene, the only thing that could have improved it is if they had a little romance dialog in there so she doesn't call you her friend. That was a bit strange.
Character goodbyes. Every.Single.ONE.. Even Javik. In fact. I was very emotionally unstable from the character goodbyes all the way through to Shepard being blasted by Harbinger. Then I went to "Wtf!?" mode to the Anderson death the back to "wtf!?" mode for the starchild scene. The when destroy happened and the ending happened and the breath scene happened. I cried non-stop for longer than at any other point through-out the game.
Then I came back on the BSN after avoiding it for months (due to spoilers) and was glad to see i wasn't alone.
Thinking about it now, Mass Effect 3 is very emotionally draining. I was going to do another full playthrough for Omega. But I don't think i will now....