Ratchet being willing to stay on the about-to-explode DreadZone station so that he could save everyone else. And his exchange with Clank before the battle with Vox was touchy too.
Even if they were asses to Ratchet throughout most of the game, it is hard not to feel sorry for Dallas and Juanita when Vox forces Deadlocked collars on them, too, and make them announce the final mission in what may very well result in their deaths. It is especially terrifying for Dallas, as he still has a lot of dreams and goals for his future, and Vox may very well be robbing him of them.
Call me sentimental, one of Zogg's final lines in the comic series made me tear up. "I'm sorry, Ratchet. I truly am one of your greatest fans."
At one point in Deadlocked, visiting a certain area on Torval will trigger Green to recall his past. He was involved in a major war and saw many of his robotic comrades, some of whom were only a few days old, and some of whom were his friends, die in battle. He barely survived said battle, and lost both legs. He was sent to a repair bot named QA-900, and fell in love with her, but their relationship was forbidden, so they had to keep their "downloads" a secret. Sadly, they were caught one day, and QA-900 was turned into a park bench, leaving Green heartbroken; he still cannot visit any parks without simulating a tear.
Despite being a prick throughout his sole appearance, Ace Hardlight wasn't always a bad sport. He started off as a Heartwarming Orphan who was eventually adopted by a group of superheroes, in which he helped out of their troubles and eventually became their leader, and ultimately, a legendary hero almost on par with Qwark. His downfall came when his home planet, along with the orphanage he grew up in and cared for so much, was destroyed. Ace was so heartbroken, that he left the superhero group that he considered as his family out of shame for his failure.
The cutscene after his battle ends with Ace warning Ratchet not to make the same mistakes as him by signing with Vox to become the new face of DreadZone, even telling Ratchet that he's the new hero. This shows that Ace has not gone completely over the line, and doesn't want Ratchet, who is also an orphan (because of Tachyon) and helped a troubled hero (Captain Qwark) get his priorities straight, to have the same fate as him.
As silly as All 4 One happened to be, one of Ratchet's interactions with Susie (a young Tharpod girl) definitely qualifies. When she's trying to mount an attack on Ephemeris — which is the reason she's an orphan — Ratchet steps up and stops her.
The after-credits scene in All 4 One: Lawrence and Nefarious are traveling through space, and as Lawrence says that they can swing by to pick up Nefarious' weapons, the doctor looks over at a photograph taken of himself and the heroes, as well as Susie, and he looks like he's ready to shed some tears...
The cutscene Ratchet's Vision from Quest for Booty — particularly the first time you play though the trilogy.
The sad fact that Ratchet had NO friends before Clank met him.
Cronk and Zephyr's deaths in "Into the Nexus".
The reactions following were all the more heartwrenching, particularly Talwyn's when you consider that they were the only family she had after her father disappeared.
Film and tie-in game
In the remake, Cora's reaction to Novalis being targeted and then after it is destroyed can be this after you find out Novalis is her Home planet.
Early on in Ratchet & Clank: Size Matters, on the last cutscene for Pokitaru, Ratchet snatches the Technomite artifact from Qwark's hand. Keep in mind that Qwark just wants to tag along after feeling sad that he doesn't know his real parents, and the look he gives after Ratchet says "Stay out of our way" is just heartwrenching.