The optional sidequest you get if you choose the Colonist background is just heartbreaking, as you have to deal with a girl who grew up as a slave taken from the same colony Shepard was born in - and is so mentally traumatized that she has to refer to herself in the third person because she can't think of herself as being the same person who was taken by the slavers. The most powerful moment is at the very end, if you convince her to take the sedative, and she says "It hurts when she....when I remember....me."
When Shepard revealed that she was a survivor from the same colony. Talitha breaks down and demands to know why Shepard isn't broken like her and wonders how s/he is able to stand up in spite of losing everything in the same brutal way as Talitha. It drove home the point to me that, given a slightly different set of circumstances, Shepard could have wound up the exact same way as Talitha.
Shepard's entire family fought to the bitter end, choosing death over slavery. All of Shepard's family were at least at some point willing fight for their lives.
I fought, my whole family fought. And got hit by an artillery barrage for their trouble. If they saw me, they probably left me for dead.
If you have Liara in your party, Noveria is heartbreaking from start to finish. She starts out excited when the Elanus Risk Control guy at the Hanshan front-desk mentions Benezia's presence, manages to stay quietly optimistic at Peak 15, and then completely loses it when you finally confront Benezia in the hot labs.
Liara: What should I tell (Shepard), Mother? That you've gone mad? That you're evil? Should I tell (Shepard) how to kill you? What should I say?!
And later, when Benezia finally dies by the team's hands:
Shepard: Hang on, we have medi-gel—
Liara: Mother! Don't go!
Benezia: Goodnight, Little Wing... I will see you with the dawn. (pause) No... light... they always said... there would be...
If you replay the first game after having played the third and having talked to Liara about what Benezia had been like, and eavesdropping on the conversation between Liara and her father, you learn not only what she'd been like but where the "Little Wing" name came from, which makes it more touching.
And then, there is Virmire.
"I'm sorry....I had to choose." "Its okay, Commander. I don't regret anything." Go ahead. Cry those Manly Tears. You know you want to.
"Fight hard, Lieutenant/Chief. Die proud!" "Aye aye, Commander."
What makes it worse is the fact that they make you choose. What the hell?! Bioware outdid themselves on that scene.
To make Virmire even worse, Captain Kirrahe's speech. Every single member of his species you encounter in the game is more or less impassive, but he delivers every line with total conviction and determination. The worst part of it is the sentence Kirrahe says to Shepard at the end, all military bravado forgotten: "Good luck, Commander. I hope we will meet again." It just brings home the reality of the situation, that in all likelihood he and what's left of his Regiment will die in the attack. Makes saving him all the more satisfying.
Captain Kirrahe: Rest assured my people will not forget what you did here. You have made an ally of the salarian people.
Captain Kirrahe: We will work together again. I am certain of it.
Salarians with their short lifespans and even more fragile physiologies only do espionage and try not to do direct confrontation in war. So Kirrahe wasn't just throwing his squad (of spies and scouts) into the fire... they were going into a situation that they weren't trained for or accustomed to: make a big noise.
Virmire is just a bigger tear jerker than the entire Suicide Mission, while you won't lose Shepard on Virmire, there is a good chance that a lot of people will die on Virmire alone and at least one of them won't make it.
Sacrificing Ashley or Kaidan is bad enough, but it's even worse if they're your love interest.
The music that plays during the debrief after Virmire doesn't help. It's the same song that plays during a romance theme, but under some conditions, it'll keep playing even after the debrief as you're walking around the ship, replacing the usual Normandy theme. It gives you the feeling that something was irrevocably lost on that mission, and that nothing from here on out is going to be the same.
Your encounter with Wrex. Having to choose between giving the Big Bad access to a nearly unlimited army of unstoppable killing machines or taking away the only chance Wrex has to save his people from a horrible genocidal bioweapon that has driven them nearly to extinction by taking their birth rates down to practically zero is even worse if you haven't done Wrex's Family Armor mission or have enough charm or intimidate points to make him back down, since there is no way to save him and knowing this is a punch in the gut.
The way Wrex stands away from everyone else and aimlessly fires his shotgun at the water as you apporach him does an excellent job to show his angst.
The final cutscene after defeating Sovereign. "Where's Shepard?" ...and then the camera cuts to that massive lump of Reaper, complete with heartbreakingly sad piano theme. Made exponentially worse if your party includes your love interest. Even knowing that Shepard wasn't really dead didn't soften the blow.
The scene becomes even more powerful if you A: romance Liara and B: take her with you onto the Presidium battle - when Shepard climbs out the wreckage, the lighting makes it look like her face is all red and puffy from weeping.
Taking Wrex is moving too. The way he hangs his head when they find them, and the way he lets Anderson steady him, then look back. For such a reserved character, seeing him crack that way...wow.
The space battle at the finale, whether you choose to save the Council or not both versions are extremely moving.
"It's the Alliance! Open a comm channel! This is the Ascension, we are taking heavy damage. GUARDIAN systems are overwhelmed, kinetic barriers are off-line..." "Captain... they've closed the channel."
And, to add extra punch to Vigil, you know that his message to you, giving you the knowledge to end Sovreign's threat, is probably the last thing that he'll do before he shuts down. Although he's a VI, he still seems to be pleased to know that he'd not maintained his vigil for nothing.
And yet, there is something awe inspiring about Vigil. He is only a VI but he and the last Prothean survivors sacrificed everything in order to give a tiny glimmer of hope to stop the Reapers forever.
"Sovereign is too strong. I'm sorry. It's too late for me. Goodbye, Shepard...thank you." Yeah Saren was quite a bastard if you have read the pre-novels but given, that in the game only he's more of a Fallen Hero and is truly sorry about his betrayal, that really is a saddening scene. Even more so when Sovereign takes control of his technology-modified body after his death and you see, that he really could not have been saved.
The sidequest on Ontarom in the first game, where you meet Corporal Toombs, the only other survivor from Akuze, holding a Cerberus scientist at gunpoint. His half-deranged and agonized ranting is heartbreaking to hear as he simply tries to get closure and justice for what they did to him. One of the most potent lines in the exchange sums it up, when the scientist calls the soldier "Mister Toombs":
Toombs: Its Corporal!CORPORAL Toombs! You don't get to lie! Not anymore!
Toombs's voice actor nailed that whole scene. You can hear the exhaustion and anguish in every line. And then the tearjerkers continue into the sequel, when you get his What the Hell, Hero? email. And worse yet, if you offer to help him recover his psyche, he is no longer traumatized, just completely pissed off. And if you spared Wayne and not Toombs, turns out The Illusive Man finished the job for Toombs.
He still doesn't understand even if you have the Sole Survivor background (both him and Shepard did suffer in the same unit, right?). Makes it even more gut-kicking.
The worst part is what happens if you're forced to shoot him. The description afterward mentions how his face is still pinched in anguish and pain. Even in death Toombs can't find peace.
If you opt to kill Doctor Wayne, there's a brief bit of post-mission exposition regarding Toombs that eliminates any hope of calm stoicism.
He opens his eyes, and you gesture to the door. He won't be left behind again.
Then there's Shepard's responses if s/he was an Akuze. If you choose the Charm option (ask Toombs to let Shepard arrest Wayne) then the Renegade dialogue to Toomb's What the Hell, Hero? response, Shepard lets forth a lot of pent-up emotion. Mark Meer gets a lot of flak, a lot of it justified, but he does this line brilliantly, mixing anger, sadness, disgust and resolution.
Shepard: You think I don't want revenge for Akuze?! Listen, Toombs. Arresting him hurts them more.
Even before that, if you pick the Paragon option in the second dialogue wheel, Shepard says that s/he didn't see anybody and that if s/he did see him s/he would have gone back to help him. You can hear the guilt in Shepard's voice.
If you allow him to shoot the scientist and Shepard was there at Akuze, a relieved but still broken Corporal Toombs mentions how records say Shepard is the only survivor of Akuze, saying "who am I to argue?" and kills himself.
When talking with Wrex about the genophage, there's this quality in his voice when he says that he can't change his people. He sounds so...resigned, so deeply, fundamentally depressed about it all. Its not obvious, and Wrex doesn't angst about it or anything, which makes it even worse. He's accepted that his species is doomed, and that they're going to go extinct, because that's what they are. It kind of quietly drives home just what it means to the krogan that their species has fallen from the height of power and turned into fatalistic mercenaries.
The brutal truth of what the genophage actually does. On the outside, it just sounds like a way to curb the Krogan's numbers by reducing their fertility, but then you read into it some more and find out that it's not actually making them less fertile in the sense of producing eggs and such; it interferes with the development of the fetal krogan, preventing every 999 out of 1000 from developing properly. It states that most krogan babies don't even reach the stage where they're stillborn. With the fact that not every krogan gets the chance to mate, the idea that even if you get the chance to try and have a kid and knowing that unless you're incredibly lucky the most you'll get is a stillborn son or daughter (and that's if you're lucky at all) is incredibly heartbreaking.
The Citadel: Homecoming assignment. Samesh Bhatia, whose wife was part of Ashley's unit on Eden Prime, pleads with Shepard for help. All he wants is to have his wife's body back to give her a proper funeral, but the Alliance is holding her body and refusing to give any explanation as to why. His reaction to the situation is heartbreaking, especially when you convince him to let the Alliance keep his wife's body for further testing. He just breaks down, telling Shepard that he misses his wife so much and he just wants her to come home.
Samesh: [after composing himself] ...Let them run their tests. Let my wife save lives, so that others are spared the loss I feel today. Goodbye. Thank you for finding me answers.
Replaying the first game is especially tearjerking while you're just walking around the Normandy. You see two random crew members, sitting together talking happily in the mess. And then it hits you, that these are the same two crew members who were killed by explosions on-screen in the intro of the second game. And what's worse is, you suddenly realise, aside from a dying scream, they never have had any lines. Two members of Shepard's crew and you never got to know them.
The VI's final message on Luna.
A burst of white noise over all frequencies nearly deafens you. Your hardsuit's heads-up display interprets it into a series of 0s and 1s: 01001000 01000101 01001100 01010000 They repeat again and again, blanketing all frequencies, until the lights on the final VI cluster flicker and die.
Why is this sad? If you decode the binary, you realize that it's screaming HELP. Over and over and over, desperately. And you just stood there and listened as it died. Worse in Mass Effect 2 if you choose the dialogue option that reveals that the "VI" was actually an AI named Hannibal, who may have only been trying to defend itself when the Alliance realized what it had become and attempted to kill it.
In ME3 it is finally revealed that your ME2 friendly AI, EDI, is actually built from the remains of the Hannibal system, softening its death somewhat
UNC: Geth Incursions has you going out and destroying Geth outposts in the Armstrong Nebula. When you complete the mission, this message appears. It seems to indicate the Heretics regret what they lost when joining Saren and the Reapers.
If the player chooses the Spacer background for Shepard, you eventually get the assignment Citadel: Old, Unhappy, Far-Off Things (If the name of this assignment sounds poetic, it's because it is. It's a line from The Solitary Reaper by William Wordsworth). While it's not as big a tearjerker as I Remember Me, poor Lieutenant Zabaleta is worthy of pity. He was sensitive, and the batarian raids on Mindoir scarred him enough that he had PTSD and turned to drinking to try and forget. But people like Shepard's mother still remember him and want to help.
A more direct example can happen if You run out of anti-Thorian grenades; if you don't ration them really carefully it's entirely possible that you'll have to end up killing a number of colonists that spend most of your time on Feros helping. If you did the water, food, and electricity missions first it's even worse; you spent your time getting the colony up an running again only to have to kill the people you were trying to help. Luckily, you can actually smash them into unconsciousness. With a good shield and fast reactions, you only need to run up to the colonists and pistol-whip or rifle-butt them into harmlessness. The game, of course, does not expound upon the potential brain damage.