Another special mention goes to when Neil Armstrong says "the eagle has landed." Cue the heartwarming montage of Mission Control applauding and Walter Cronkite with a big smile on his face, with Steve Jabonsky's score added to the mix.
Ron's line of "I will follow you till the end of time" as he and his wife Judy are giving Sam a pep-talk after he had an argument with Carly tugged a bit at the heartstrings. Shows how much in love they were and still are.
Despite everything that is going on around them, explosions, Bots and humans all fighting to the death... and Sam's number 1 priority in this Hellfest-keeping Carly safe. You can tell she's visibly worried if they're going to make it out of this alive, and Sam tenderly grabs her face and tells her, "You're gonna be fine. I promise."
Before everything goes to hell (well, more to hell), there's a bit where Sam and Bumblebee are in his apartment and Bee is crouched in robot form and Sam is just talking to him. It was just a sweet moment, especially because it was the first time that you really ever saw them like that.
On that note, just the visual of Sam with his hand over Bee's mouth had this troper wibbling a bit.
A small one, but Optimus meeting Buzz Aldrin. Buzz shows him respect and Optimus returns it. It's small, but Optimus shows respect to this human because he understands just what he did for his race.
Optimus: The honor is mine.
You mileage may Really vary on this one, but right before the final fight scene, we see Megatron, defeated and broken, lying against a building. His authority and power, which is all we've ever seen him fight for, has vanished. And all he does is look up and say:
Megatron:Cybertron, at last you are saved.
In that moment, we see him for what he is deep down inside: a being who's lost his first home to destruction, and just wants to fix it again. In that moment, for this Troper, at least, Megatron might have redeemed himself a bit in his eyes. Which makes seeing him die, for sure this time, with the object of all he's worked toward fixing imploding into oblivion... it's almost a Tear Jerker.
In the adaptations, he's completely serious about the truce he offers. Optimus accepts, and they unite the remaining Transformers to head off to rebuild somewhere else. Two brothers, torn apart by war, finally reunited for the same cause.
YMMV, but Sam and Carly running into each others' arms at the end of the movie. You can tell how happy and relieved they both are they made it out of this alive.
A small but notable one; Megatron feeding the hatchlings at the beginning of the movie. No malice or evil intent there, just a father trying to provide for his children. D'aww.
The Autobots' vow to stay and fight when they arrive to Chicago.
Leadfoot: We ain't goin' nowhere.
Brains: Yeah, no one's exilin' us!
Wheelie: The Autobots are staying right here. We're going to help you win this war!