Early in the game, if you check the emails on your computer, one email is from your friend Diane had your beloved dog put to sleep because she thought you had died from your injuries. Puts all those shattered mirrors in a very harsh and heartbreaking light.
Even without that email, the mirror counts. It shows that Jensen is clearly not in a happy state of mind about his Augmentations, and the reflection mirror is a constant reminder of what happened (The post it note suggests that this wasn't the first mirror he'd smashed in anger).
Worse yet: If you hack into the computer in Jensen's apartment building's lobby, you can find out the mirror has arrived but no-one's bothered to pick it up yet. Makes you really feel for the guy, huh?
The endings, in which Adam reflects on humankind and his life while real video footage is shown to emphasize his points.
If you choose the self-destruct ending, after the screen goes black, you can hear creaking and groaning as the entire facility gives in to the overwhelming pressure of oceanic water, and unless you mute it, you are forced to listen to Adam's last living moments.
You return to Detroit and the riots have broken out. After playing the first game and reading that aug research had disappeared in the face of controversy, and augmented humans were heavily discriminated against, you realize at this part in the game that it's all downhill from here. You are literally watching the world collapse from within, and it's all a long, slow slide to the first game's Crapsack World.
Malik's murder. You've been depending on her three fourths of the game, and she's killed, execution-style, right in front of you after her Heroic Sacrifice to buy you time to escape.
His reaction as he hears the gunshot and sees her body sink to the ground speaks volumes.
Adam: You bastard!FARIDAH!
Others just accepted the devastating moment and let it flow into the story and Adam's mental state.
Some players didn't even realize that her death was preventable as they had been trading fire with the mercs since the section began.
To add even further insult to injury, you can also find Malik's corpse in an operating table in the Harvesters' hideout, meaning Belltower sold them her corpse to be stripped for augmentations just like they did with Sevchenko.
The other possible way for her to die, namely the explosion of the VTOL once it soaks too much enemy fire, leads to an arguably even more tear-jerking exchange:
Adam: Malik...Malik, you hurt?
Faridah: *gasps in pain* Just a scratch, Spy Boy. But I think...*gasps again* I think you're on your own now...
Faridah: Give em hell for me. *VTOL explodes*
The battle with Hyron. Or more specifically, the part where if you're not clever enough or packing enough nonlethal weaponry, where you realize you have to kill the Hyron Drones.
IIRC, all you have to do is keep hitting the drones with nonlethal weaponry or use the laser rifle on Zhao. The ending doesn't change, but you don't have to kill them.
You can also use Darrow's code (if you got it) on the console directly in front of Zhao.
The entirety of Hyron and its' role in the end. Where to even begin?
For one, if you look at the end of many of the messages on computers or pocket secretaries in Panchea, there are small messages at the end referencing a 'mother' and 'father'.
If you listen to the drones' ranting, they frequently spew dialogue about a mother.
And then there's Hyron's original purpose. They created this machine and linked people INTO it, to drive all augs insane and cause widespread panic and bloodshed.
In "The Missing Link" DLC in the secret laboratory area of Rifleman Base, you come across a young woman named Nina Sullivan, who is all of 20 years old and scared out of mind. While you can talk with her to and get information, due to your current circumstances, you're in no position to help her, despite her frantic pleas. Then there's an Oh, Crap moment when you are on your way back out, and she is gone. Turns out a very speedy guard transferred her back to the main cell block, and she's one of the ones you can choose to save.
In the police station when access to the morgue is needed deciding to be social and getting access through Wayne Haas by choosing mostly Plead and choosing Absolve once was the epitome of a tear jerker.
What must be Faridah (if she's alive) and Frank's reactions if Adam chooses to destroy Panchaea, once the news reports what happened. Their boss is gone, a whole bunch of people are dead — likely some of them were Sarif employees as well — and Adam, whom both of them had grown close to over the course of the game and clearly cared about (whether Frank would ever admit it or not), is gone. Frank had just expressed apprehension over Adam going it alone. And what happened? Adam died, along with hundreds of people. There's no way for them to know that it wasn't Adam's failure, no way for them to know if either of them could have saved him or Sarif or anyone else had Faridah been there with her aircraft, or had Frank been in contact with Adam. ...And they probably won't have jobs anymore, since Sarif will likely go under in short order. The only consolation, ironically enough, is that they won't ever know that it wasn't Adam's failure, but rather his choice to kill himself, Sarif, Darrow, Taggart, and hundreds of innocent people.
They would also become some of the few people left to actually know something about went on but will also be incredibly vulnerable against the growing conspiracy. Especially with the information that Megan had to have handed to Bob Page, it's likely they didn't survive more than a few months.
Not so much an outright tearjerker as just something that is genuinely saddening is some of the comments people will make toward Adam due to his augmentations. Some aren't outright mean, just misguided. Others... not so much. It's even worse because Adam never asked for this.
"Why did you do it? You were beautiful just the way you were. You poor man."
"I don't mean to judge, but I think that people who choose to augment themselves are rejecting their own humanity."
"Nothing personal, but I don't want to have anything to do with you."
"What are you looking at, pal? Scanning me with those metal eyes of yours?"
"Look, I don't have anything against you, but just stay away, okay?"
"No offense, but if it were up to me, this place would have a No Aug policy."
On the other hand, every single one of those people who said those horrible things to Adam? You can retort.
From The Missing Link DLC, there's Keitner's death. She was trying to protect innocent people, and even at the end begs Adam to save Dr. Kavanaugh so that no one else will be stolen and experimented on.
In a way, the Foregone Conclusion awaiting beyond the endings. If Adam lets Darrow's message out the people will learn of the Illuminati's existence and give up a promising technology in a desperate attempt to keep their freedom...only to be ruled from the shadows twenty five years later. If Adam trusts the Illuminati to be the leaders the world needs, they prove incompetent at their self-appointed task and let the world slide into Hell. If he trusts Sarif to defeat the Illuminati, then his boss fails and the Illuminati's successors find a way to control augmentation after all. If he kills himself and everyone in Panchaea, trusting humanity to make the right choices...it doesn't. No matter who Adam trusts, they will inevitably let him down.
A minor one, but searching the pods in the Alice Garden Pods during the first Hensha visit, you can find a email from a father to his daughter, describing his business trip as glamorous. Presumably not to worry her.
The last exchange between Jensen and Pritchard. He really cared about Adam's well being all along. It gets sadder if you think about the self-destruct option being the real ending
While in the Hengsha Court Gardens, some of the notes you can find in those single-person beds are downright heartbreaking. Particularly the email from a husband to his wife and child talking about how glorious everything is and how well he's doing, and another one that's essentially a suicide note.