Starscream's stealth kill animations. They include him tapping the victim on the shoulder and slapping a bomb over his head or kicking them square in the gearbox, then sticking a bomb onto them, all while laughing impishly.
In a scene where Starscream stealth kills two mooks, you can hear one of the mooks shaking with a very cartoonish sound effect.
The credits have a few hilarious bits, including Bumblebee dancing to music provided by Soundwave and Metroplex playing with the bodies of Transformers as if they were toys.
Of all times, during the epic final battle, Optimus and Megatron decide to engage in Snark-to-Snark Combat.
Megatron: Impressive for a data clerk... you should've spent more time in the pit!
Optimus: Well, you should've spent more time in the library!
The Shout-Out to the G1 Movie in Grimlock Smash is very nostalgia driven funny. Kickback is about to make his escape, only for the door behind him to land on top of him. Out strolls Slug in triceratops mode, who pauses and says, "Excuse me."
Grimlock and Slug arguing after the former finishes off a group of Insecticons.
Slug: You cut through those guys like Beryllium Bologna!
Grimlock: You mean Cesium Salami!
Slug: No, Beryllium Bologna!!
Grimlock: Cesium Salami!!!
Another funny and awesome, moment occurs when Grimlock sees Slug charge a Bruiser. Grimlock shouts "Slug, look out, those things are toug-" but Slug effortlessly flings the Bruiser aside before he can finish. Grimlock then gives a Flat "What." and says "Never mind."
This little conversation between Vortex and Brawl, with Onslaught telling them to shut it right after:
Vortex: Whoa, it's spooky dark down here.
Brawl: You're afraid of the dark?
Vortex: Well, it does kinda make it hard to see.
In the beginning of the final chapter:
Decepticon Soldier: Yes, sir.
Vortex: Yes sir, what?
Decepticon Soldier: Yes sir — sir?
When Jazz first meets Bruticus:
Jazz: Whoa, Bruticus, you're even uglier up close.
And later, when Bruticus breaks out his rotor-shield:
Jazz: You don't think I'm coming near that, do you?
Hey, Bruticus does have Swindle for his right leg.
When Bruticus is attacking the energon transport:
Autobot soldier: He's going after the turbines!
Bruticus: Nope! It's just in my way!
Optimus is cornered by three leapers in a narrow hallway, enemies specifically difficult to kill from the front and Optimus knows it. As they loom over him, Metroplex's fist comes through the wall and crushes them. Both Prime and Metroplex just share a brief nod to each other and continue on. Also counts as a Moment Of Awesome for Metroplex.
Metroplex repeatedly smashing Megatron into the rubble. Fully controllable by the player. Like the above, it's also a Moment Of Awesome for the big guy.
Especially funny since during Megatron's monologue towards a captured Optimus, none of the cons notice a giant, hulking cityformer rising up behind the window until the last second.
The banter between Cliffjumper and Jazz, especially in the latter's mission:
Jazz: Cliffjumper, you catch any of that?
Cliffjumper: You mean the screaming? The horror? Followed by more screaming?
Jazz: Uh, yeah. That'd be it.
Finding the crown in Starscream's level, which he will then proceed to wear for the rest of the time you play as him. It's made even funnier once you switch from Starscream to Grimlock because one of the first things you can do once you're in control is destroy the crown by stepping on it, much as Galvatron did in the movie.
A brief but funny moment in Jazz's mission— he and Cliffjumper come across a locked door in a Decepticon facility. It scans them with a beam and a robotic voice intones, "Access denied," to which Jazz simply responds, "We'll see about that!". He then proceeds to pull down the door with his grappling hook, and as the two of them stroll on through, the door says "Access denied" in a warped, wavering tone of voice.
Another one from Jazz's mission: At one point there's a locked door and a lever that can take you to a weapon stash. Instead of the lever simply opening the door, it transforms, does the Carlton dance, and then the door behind it explodes.
A lot of the prompts are either awesome or ridiculous. A good one is when you're playing as Megatron and are about to reclaim your leadership from Starscream. A prompt comes up that simply says "Shut Starscream Up". You can let the guy monologue for a little while too, to heighten the effect.
Some of Teletraan-1's comments can be surprisingly funny. There's noting quite like hearing it drone "Stay smooth, Jazz" in its monotone voice. Of particular note is his comment to Starscream in Chapter XI:
''Projected odds of survival are extremely low."
And of course there's what it says to Swindle:
"''It is unlikely you will survive Starscream's leadership."
And it notes that Cliffjumper is on probation.
In the last part of "Starscream's Betrayal", when you first get to be Grimlock as you are passing through an outer hallway with bars as the walls, look down and you will see a Decepticon that got stuck trying to escape through the "window". The best part is that he has wheels and has apparently decided to take his chances with gravity rather than Grimlock.
You can head into Grimlock's room to watch TV. As Optimus, of all characters!
If you end up missing all the homing mines on Vortex's level, Blast Off has something to say about it:
Blast Off: You plan on shooting any of them today, Vortex?
Vortex: Hard to get a bead.
Blast Off: Aim with your guns, not your mouth.
In Cliffjumper's chapter, you can choose to lose your stealth at the trash compactor and take out 'Cons the hard way. A pair of shotgunners come out of a room filled with Energon storage boxes and... a pin-up poster of Arcee. Cue you having a second look just to be sure of the color scheme and chassis.