A lot of the flashbacks, particularly the final ones when Wheatley was so close to finally getting the courage to ask Chell out (being so dedicated in trying to get his 'speech' just right) only to be taken by the Scientists one final time. Basically anytime he was in the scientists grasp was just heartbreaking knowing what they were going to do to him.
Seeing as it focused the most on the flashbacks Chapter 8 was full of tearjerkers: Chell leaving a bagel for Wheatley on his desk everyday even though it seemed he wouldn't be returning anytime soon, as well as her seeing such a long gone version of herself in Wheately's memory, and notably the description of Wheatley being painfully stripped of his own memory and just...wanting to go home:
"And now this, this didn't hurt but that didn't make it any better than the pain, this feeling, this unbearable draining tearing sensation, huge important chunks of who he was ripping away into the dark like shards of glass from a splintering pane, and he didn't even know what they were because once they were gone, he could hardly hang on to the fact that they'd ever been there at all. And all he could think was pleasepleaseplease nononononono I want to go home I want to go home please- and now he didn't know where or what 'home' was but the thought persevered, a senseless desperate litany of I have to get out I have to get out I have to I I I-"
Wheatley's painful reaction upon realizing he used to be a human and feeling he has now has even less of a purpose than he previously thought. Pretty much whenever Wheatley's depressed or upset was just heartbreaking.
One of the short sequels is about Wheatley dealing with his libido. This sounds like it should be funny, right? Wrong. The only thing Wheatley has to compare the feeling to is the programmed itch that drove him to attempted homicide. He hates himself for it, and drags himself into a cold shower, biting and clawing at himself to try and make the desire stop.