The montage of the Autobots meeting up on Earth, particularly for the music.
"The Gathering of the Autobots" really climaxes when Ironhide rises out of the swimming pool - a gentle choir singing in the background - and the little girl looking at him without any hint of worry or fear. "Children, sleep safe at night. The heroes have come to watch over you".
And the finale, with "What I've Done" in the background, Optimus' final monologue, declaring how they will protect humanity.
Prime asking Ironhide, "Were we so different?", who declares with sincerity uncontaminated by cynicism and irony that "Freedom is the right of all sentient beings."
The distant look Optimus has when he responds to Ironhide; it's pretty easy to imagine that he was remembering all the brutality he saw during the Great War.
Bumblebee's capture, especially when you see him being experimented on, all the while making muffled whines in pain.
Equally gut-wrenching is Sam trying— unsuccessfully— to get Sector Seven to stop attacking Bumblebee.
Sam: Look! He's not even trying to fight back! ... Stop hurting him!
How about the first time Optimus Prime is in robot mode on camera for the first time speaking to Sam and Mikaela? The first line of dialogue that he speaks is so characteristic of him, and with the voice of Peter Cullen to this day will still cause tears of nostalgia fore many.
The fact that it was easy for Megatron to tear him apart was tearjerking in and of itself. Not to mention the fact that he died trying to protect some random humans when he could have easily run away and saved himself. He died a true Autobots death, he died a hero.
Transformers: Revenge of the Fallen (2009)
Optimus Prime's death is a big one even when you know it's coming.
Ron Witwicky's heartrending cries when Sam is (temporarily) killed by Megatron.
Even before, with Sam telling his father: "You've gotta' let me go. You've gotta let me go." Especially contrasted with how eager his dad was to ship him off to college in the beginning of the movie.
Bumblebee's own reaction to Sam's death.. All he could do was whine with terror anguish. He couldn't vocalize his feelings.
YMMV like crazy on this, but the scene where Megatron watches in horror and anguish as Optimus kills the Fallen could count. Watching Megatron, of all bots, express sadness over anyone is jarring, but then one has to remember that, for all his flaws (and there are MANY of them) Megatron isn't necessarily a soulless monster...
Transformers: Dark Of The Moon (2011)
Optimus's ending speech, which ends with "But the day will never come, that we forsake this planet and its people" . Cue Iridescent by Linkin Park playing over the end credits.
The novel ends on a line afterwards: We are here. We... are home".
Que/Wheeljack's death. Poor guy, just trying to negotiate...
Worse is, we barely even knew him, since he'd been in a total of two scenes actually doing anything, but his line before it happens.
"Bu-but-but, we surrender!"
Sight of Bumblebee about to be executed. Made even more dramatic by the fact that there didn't seem to be any hope of him being rescued and another Autobot was just ruthlessly slaughtered right then and there! What's even worse is Bumblebee reaching out to Que/Wheeljack's corpse, making it clear that he'd just seen his friend get murdered!
Even worse is when Bumblebee speaks, not via radio, but actually speaks during the scene. When Que died, he said "Good bye, old friend." and when he sees Sam, hiding and unable to do anything to help him, "We had a good run."
To add on to the impact, the track "No Prisoners, Only Trophies" plays soft and gentle, more suiting to quiet and reminiscing-type scenes. It adds on to the helplessness of the sequence.
Manly Tears may be shed during the opening sequence with the moon-landing. And maybe again when Buzz Aldrin shows up.
When the Autobots were forced to leave, thanks to the world leaders, Optimus and Bumblebee say their goodbyes to Sam.
Also what doubles this scene making it into a tear jerker the Decepticons are holding Carly hostage, and will kill her if Sam doesn't do as they say, which is essentially be a spy for them against the Autobots. Prime already had one long time friend betray him, so in hindsight when he calls Sam his one true friend, you know Sam felt like he was punched in the gut! The kid loved and respected the Autobots, he especially respected Optimus, so he was forced to momentarily betray his friends, in order to keep Carly alive.
It does not help at all that "There is No Plan", which is basically a very mournful version of "Arrival to Earth" plus "Optimus" from the first film's score, plays in the background while all this is going on.
When Wheelie and Brains board the Decepticon cruiser and take it down, during the crash, one of them says that they're not going to make it. After the cruiser goes down, they're nowhere to be seen, meaning that they were right. What hammers the point even harder is that Wheelie was one of the few people that was genuinely nice to Brains to begin with.
It's subtle, but look at the expression on Optimus' face after he executes Sentinel Prime. It's quite clear that doing that deeply affected him, as he essentially had to put a gun to his mentor's head and pull the trigger. It's one thing for Optimus to kill Megatron. Megatron was his avowed enemy and had caused nothing but death and destruction for centuries. But Sentinel was his friend and Optimus' mentor, the one who taught him the very thing he's now killing him for.
Sentinel's final cry of "No, Optimus!" right before Optimus kills him was pretty depressing. It would be different if it was someone like Megatron or Shockwave, but as mentioned above, this is the only father figure Optimus has ever known. And he has no choice but to make him pay for what he's done.
Hearing Optimus Prime say "Please..." after Sentinel cuts off his arm and drags him across the ground to finish him. Bay made it clear beforehand that anyone who dies in this movie isn't going to magically come back, and in that moment, it really felt like Optimus might die. The fact that he would plead with Sentinel one last time, hoping to revive the goodness in his old mentor, was almost too much to handle.
Seeing Cybertron dissolve into a black hole. Cybertron, the Autobots' (and Decepticons') home, lost forever.
Worse (or better), remember what Megatron, his authority and power, all we've ever seen him care about all but gone, said:
Megatron: Cybertron, you are saved... At last...
He's not just a power hungry tyrant: he's a living being like us, who wants to see his first home made whole again. He actually showed that he cared for something other than himself. In this tropers eyes, he just might have redeemed himself a bit for all he did leading up to that moment. And then... he and his home are gone. That which he worked for, the cause he championed, such a pure end for such horrific means, he lost it in his final moments. Even for Megatron... it just doesn't seem right.
The final fight scene between Optimus and Megatron has been criticized for being to short... has no one considered that maybe Megatron didn't want to fight anymore? His body wrecked, his home destroyed, everything he ever aimed to accomplish rendered moot, and everyone he ever cared about dead... except for Optimus. In one final, desperate attempt to save himself, well aware of the atrocities he's committed, he turns to Optimus and asks for forgiveness... and finds that Optimus has none left in his Spark for the likes of him... Is it possible that the leader of the Decepticons reached the Despair Event Horizon and just... gave up?
For some, when Sam starts to walk out of his Accureta Systems job interview. He says pretty much what he says there a few times, but that's the first time you see how much he really wants to do something that matters.
Within seconds, not only did Sentinel betray the Autobots, but he killed Ironhide in a brutal and horrifying manner, which comes completely out of nowhere. Even more shocking is that Ironhide wasn't a new character introduced in this film, but one of the Autobots from the first film whose been in all three, a character we actually got to know...
What's worse is Ironhide's reaction as he's dying. It's clear he's just as shocked as the audience probably is. He didn't die in battle with an enemy - a friend that he looked up to and respected suddenly shoots him in the back and murders him.
For a Decepticon lover, the deaths of Starscream, Soundwave, and Megatron.
The deaths of Skids and Mudflap in the comic adaptation. Despite their controversial characterization, it's hard not to feel sad as Mudflap flies into a grief-striken rage over his brother's death and is himself killed moments later.
The novel arguably makes it worse with Mudflap's reaction to Skids' death:
"There had never been a moment when the motor-mouthed Autobot named Mudflap had been at a loss for words. Under ordinary circumstances, Sam would expected him to say something like "Oh, no you did-unt! Oh NO you DID-UNT! Uh uh! You in it now!" He said nothing like that. Perhaps it was because of the psychic link that he shared with his twin so that he had actually felt Skids die. Perhaps it was because of the betrayal of a warrior they revered above all others, like finding out the Archangel Michael was on Satan's payroll. Whatever the reason, Mudflap didn't react the way Sam would have expected. Instead he howled. It was a primal agony, torn from the individual bit of Spark that powered all the Autobots. It was the most horrible thing Sam Witwicky had ever heard, and he recognized it for what it was: the sound of a soul dying. And then it escalated into a war cry of undiluted fury."
"When you were standing in the wake of devastation... when you were waiting on the edge of the unknown... and with the Cataclysm raining down, insides crying "Save me now", you were there, and possibly alone..."
Some people criticize Carly's character for being useless, not contributing much, only being in the movie to look pretty, etc. and in some ways she does come off as clingy. She doesn't want Sam getting himself involved in any more alien robot battles, even though he spends much of the first part of the movie trying to get right back into the middle of things. It wasn't until the scene where it looks like Carly and Sam have a falling out and she ends up taking back the 'lucky rabbit' and leaving Sam with the torn off foot that a motive behind Carly's seemingly clingy character emerges. It's a small, quiet, blink-and-you-miss-it type line that she says to Sam, which is something like "Do you think I'd rather have that medal instead of my brother?" Carly's behavior towards Sam suddenly makes perfect sense. Her brother was a soldier who died in combat, and she doesn't want to go through that pain again by losing Sam. No wonder she looks so stunned and horrified during that iconic scene where she stares at the battlefield that was once Chicago: She's seeing the exact type of conditions that killed her brother.
When the Autobots ship is blown up.
Optimus flying into the battle scene after the other Autobots escape from Soundwave, with the track It's Our Fight playing in full blast, and watching Optimus destroying Decepticons left and right before tearing Shockwave apart.
Optimus's last words to Sentinel Prime before he executes his mentor. The tragedy behind those words is how true they are; Sentinel was the one who taught Optimus that freedom is the right of all sentient beings, and Sentinel turned against and betrayed those words in "Dark of the Moon".