ME1: I have to say that I'm a pretty big wimp when it comes to these things, but when on my first playthrough, I decided to sacrifice the council and...:
"It's the Alliance! We're taking heavy damage! Guardian Defences are overwhelmed...!" "..They closed the channel..." The way that Joker hesitates before turning off the comm, and the utter loss of hope on their faces, I really wanted to reload. Major lump in my throat.
The crazed Akuze guy; he confides in Shepard (and co.) his experience with Cerberus, all the horrible things. The hope that returned to his face when he found it was Shepard, and when Shepard realizes he survived Akuze. It's really sad if you let him get revenge on the doctor (he said "Please! We didn't have a choice!" right before he died, and I believed him...) Toombs experiences a small measure of peace before announcing "The vids say you're the sole survivor of what happened on Akuze. Who am I to argue?" Then he shoots himself. Powerful stuff.
Saren redeeming himself via suicide, he seems sincere, and the way he gives his regards to Shepard.. so sad
Of course, the obligatory Virmire. I had been spoiled before about the sacrifice, so I already determined who I was going to leave. Yet when the decision finally came up I literally spent 5 minutes battling with myself if I was really making the right choice. Then the knife twisted after I rescued Ashley at the towers:
Shepard: Don't worry Kaidan, we're coming back for you.
Kaidan: I think we both know that's not going to happen.
The way he just calmly and unapologeticly accepts his death...it's heartwrenching
ME2:
On Illium, the Salarian and his asari step-daughter, shopping for keepsakes so his asari family will remember him ong after he's passed away.
Miranda and Oriana finally meeting. You could really tell Miranda loved her, and how she displayed reluctance despite really wanting to.
I too, am an unfortunate victim of Miranda's advice. I lost Grunt (my baby!) to the swarm...

<-- My face
The prisonor next to 'Benny' on Purgatory, he sounded so nice and innocent, He seemed so pitiful and reasonable.and I honestly would have considered the option of buying him had the option come up. Until he mentioned he killed 10 people. I immediately felt disgusted with myself for having considered it.
Reading Garrus' Shadow Broker profile. He needs credit for his deeds Damn it! Also Miranda's, the perfect woman...except she's unable to have children. And the way the built it up with the dating sites made it clear that this is something she desperately wants.
I'm a sap, and fangirl, so Garrus' 'love' scene. "I want something to go right...Just once...just..." They can't show much conventional affection physically (lest Garrus rip Shepard's face off or something), so it seems like a powerful moment when Shepard reaches to caress his face and they 'bump heads'.
Silly, but it broke my heart to have to tell the krogan on the citadel that there were no fish in the presidium.