I'm too lazy to pick out every specific scene, so I will name general missions as well as some stand out moments...
Citadel DLC, ME3
Lair of the Shadow Broker DLC, ME2
the series of assignments that lead up to the Javelin Missile assignment, ME2 (N7: Archeological Dig Site, N7: MSV Strontium Mule, N7: Blue Suns Base, and N7: Javelin Missiles Launched. ME4 would be my favorite ME game for sure in terms of side quests if it has a LOT of series of assignments like that, but with the story telling of the ME1 assignments.)
Ilos and conclusion, ME1
Tuchanka, ME3
Overlord DLC, ME2
Paragon Control and the epilogue showing how most of my decisions affected the whole galaxy [sorry, but I like this ending so long as I don't think too hard about it and the moment before choosing.], ME3
Kasumi: Stolen Memory, ME2
that feeling I got when I got every achievement on my Xbox 360 AND every trophy on my PS3 copies of ME2 and ME3.
Saving David Archer from Gavin's torture in Overlord, ME2
Seeing David Archer in Grissom Academy after saving him in ME2, ME3
Grunt's day off, ME3
Grunt's sacrifice, then survival in that Rachni mission, ME3
"That was for Thane, you son of a ******!", ME3 [last time I played ME3, I skipped going to see Thane and Miranda died in Sanctuary, and so instead, he said "That was for Miranda, you son of a ******!"]
Been a while since I played ME1, so I can't remember many specific moments [outside of your typical answers such as when you became a Spectre]