My all time favourite moment from the ME trilogy is the citadel run from the end of the first game. When you come out of the conduit and fall out of the mako, deal with the geth and ride the elevator up. Just when you think, "I'm heading into the final fight" the elevator stops. Wasting no time shepard just says, "Suit up!" and blows out the window. Every time the camera pans outside and views the closed citadel.. it's incredible. To me, it's awe inspiring (the citadel) and demonstrates the persistence and undeniable will of shepard.
That said, so may excellent moments mentioned in this thread. Mordin's final scene, the shifty cow, talking with sovereign and harbinger, etc. I think my second favourite moment (also comes from the first game) is the drop on Ilos. When your crew is just arguing and fighting within itself and shepard just quiets everyone as joker says, "I can do it". Amazing.
I'm partial to ME1 for all my memorable moments. Probably because I was completely blown away by it at the time (and still). For me it has the best ambient sounds and music in the trilogy. ME3 has the best sound effects though. After battlefront, I'm excited to hear ME:A.