One great moment is seen in part 3 of "The Ultimate Doom":
Shockwave: "You cannot get out!" [Shockwave unleashes a massive blast, but blows a hole in the wall instead of Skyfire] Skyfire: "I can now!"
Just before that, Brawn, Bumblebee, Spike and Sparkplug are running through an installation on Cybertron trying to get to the surface. Brawn shouts, "I'll get the door!" He then proceeds to run through it.
The drunken Decepticon scene in "Microbots":
Megatron: "Decepticons: a toast. To the imminent destruction of the accursed Autobots!" (The Decepticons begin drinking Energon) Starscream: "Energy! We won't need to conserve it after tomorrow. We can bleed this planet dry!" Rumble:[hiccups] "Boy, these are good. [hiccups] I needed to refuel. Energy!" Megatron: "Energy! Energy!" Thundercracker: "Hey! This stuff's the greatest! [passes out]" Megatron: "Ah, those were the good ol' days, back on Cybertron...Didn' have to...sneak around in these...ugly Earth disguises." (Powerglide arrives) Powerglide: "Time to cut the jets and glide!...What in the world?" Megatron: "Good ol' Cybertron! Land...of the metal moon!"
Heck, even Laserbeak of all characters is so smashed he barrel rolls into the ground when trying to pursue Powerglide.
While it results from a scale error, the scene of Hoist driving Huffer in "Make Tracks" gets me every time... especially because Huffer's toy is tiny compared to Hoist's.
In The Autobot Run, Skywarp has just frozen the Autobots in their Automobile Forms with a weapon called the Transfixatron, and the Autobots have just found that out:
Sunstreaker: I can't.... change back... into my normal handsome self!
Megatron: (Flies in to rub salt in the wounds) It seems you Autobots have a slight "Identity Problem?" Huhuhahahahaha!!
When the Mêlée à Trois between Megatron, Starscream, Devastator, Blitzwing and Astrotrain finally occurs there are two different dialogues.
Thundercracker, Ramjet and Thrust have a pool:
Thundercracker: I say Megatron will prevail!
Thrust: Three energon cubes say you're wrong!
Thundercracker: Make it four!
Ramjet: My money is on Devastator.
The Autobots save Optimus and are amazed.
Trailbreaker: Your friends are waiting for you!
Optimus Prime: (chuckles) I never get involved in domestic squabbles.
Ironhide: I think we'll need a program to follow the players.
Blitzwing mistakes a football coach for a military officer and drafts him as his advisor. After he gives some surprisingly good advice, Blitzwing thanks the guy and stuffs him into a locker. When the episode is resolved, it is not shown what happened to him.
Astrotrain brings a bunch of trains to life as his "Astroforce". He leaves them alone for a few minutes and they've somehow derailed themselves and gotten tangled in a knot. Then one charges and breaks a water main that ends up flooding the city.
In the beginning, Starscream, Blitzwing, and Astrotrain carve their faces along with Megatron's into the side of a mountain Rushmore Refacement style. Then, they destroy Megatron's face.
Season 3, "Webworld". 3 words: Galvatron. In. Therapy.
Therapist: "Galvatron, don't fight it. Just say whatever comes to mind." Galvatron:"Kill! Smash! Destroy!" Therapist: "Err...yes, go on" Galvatron: "Rend! Mangle! Distort!"
Galvatron: "I hate the Autobots! I hate Cyclonus! And I'm not very fond of YOU, either!"
There's also the bit when the administrator makes Cyclonus validate all the paperwork.
Administrator: "There, that's your copy."
Cyclonus: "..." *rips receipt*
Cyclonus: "It will take the Torkulons centuries to rebuild."
Galvatron: "Only CENTURIES?!?!" *tosses the administrator aside in disgust*
Galvatron asks one of natives where the Autobots are. The creature answers in gibberish, and Galvatron calls him an idiot.
Galvatron:[panting in barely restrained rage] "Fleshling, I warn you...tell me where to find the Autobots or—"
Inmate: "Mommy!" [licks him with an absurdly long tongue]
Season 2, "Sea Change". Using a magical metamorphic spring, a cute alien chick tricks Rumble into becoming a tree.
In "Prime Target", Optimus finds himself on the grounds of an Egomaniac Hunter who wanted to add his head to his collection. Astrotrain and Blitzwing stumbled upon this and shadowed Optimus. When Optimus bypassed an Obvious Trap, Blitzwing ends up triggering it himself, and Astrotrain has to blast him free of it.
Optimus Prime: "Amazing. A booby trap that actually catches boobies."
Lord Chumley's butler gives some really good deadpan snarker answers.
Lord Chumley: "Darn those Decepticons! Always ruining my fun!.'''
Dimsworth: Yes, much like the Humane Society I suppose...
In "Child's Play," Prime has absolutely zero patience for Perceptor's Expospeak Gags. Twice in a row, when he's trying to explain how he can technobabble the Autobots back home, Prime cuts him off by simply saying, "Perceptor, just do it."
And the second time, he says it faster and in a completely flat monotone, as if he's thinking, "I just said..."
In the same episode, the Decepticons are being waylayed by the (proportionally) giant cat and fish of the alien boy whose room they materialized in. Optimus's response when it's pointed out the 'Cons are getting mangled? "Good! Now let's get out of here."
When the Decepticons make it back to Earth, Thrust complains about landing in a swamp. Starscream tells him to be thankful they're no longer on a world of green monsters... then they get grabbed by alligators and pulled under the water. Starscream screams, "Get this thing off me!"
Ultra Magnus in season 3's "Fight or Flee":
"I've never seen anything this beautiful in the entire galaxy." (beat) "All right, give me the bomb."
In "Countdown to Extinction", Megatron, Skywarp and Rumble (or Frenzy) exit a cave they've hidden the elements to their latest plan in. Optimus manages to blindside Megatron, uppercutting him up onto a cliff face.
Megatron: Here, have a ton of fun! [He tosses a boulder at Optimus]
[Optimus dodges out of the way as it hits Frenzy (Or Rumble). Prime chuckles heartily.]
Optimus Prime: Your aim's improving, Megatron!
In Season 3's "Ghost in the Machine", Starscream's ghost has abandoned Astrotrain after possessing him in order to get to Cybertron (and Unicron's floating head). The Autobots shoot him down (thinking he was bringing an assault force) and bring him in for questioning:
Rodimus Prime: "Why did you attack Cybertron all by yourself? Are you stupid or just obedient?"
Another winner from that episode involves Starscream's ghost, again, this time possessing Scourge...or the half of him holding a gun, anyway.
Scourge: "Give me that blaster!" Starscream: "No! Get one of your own!"
"Changing Gears" has cranky Gears becoming friendly in a passive-aggressive way after one of his chips was taken out.
Gears: "I should be very angry at you Megatron. You are an evil son of a retrorat, but for some reason, I just can't get too upset."
Gears: "How can I help you, Megatron, heh heh, you rotten hunk of scrap?"
Then there's Ironhide's reaction on seeing said cheerful Gears.
"What did you do to Gears, you monster? You turned him...nice!"
The Decepticons get their just deserts in "The Immobilizer".
Megatron: The most important thing is that I get what I deserve! And I always do. [the water beneath the Decepticons returns to normal, causing them to fall into it and be washed away by the river] Trailbreaker: You deserve that alright, Mega-jerk! Rust in peace! [The Autobots laugh]
The Decepticons try to use a mind probe on Astoria to learn her father's formula. We get this gem:
Soundwave: Subject's mind ... completely empty. note The wires had slipped loose
Astoria manages to annoy Megatron to the point he ends up losing his temper and shooting the mind probe with his arm cannon.
Really, this entire scene, with the Decepticon's massive frustration with Astoria's attitude and her Walking Techbane tendencies affecting their equipment, is such a CMOF that it's worth how ludicrous the rest of the episode is. Watch it here.
In "Megatron's Master Plan", a kid idiotically asks Laserbeak, "Laserbeak wanna cracker?" Laserbeak doesn't say anything, but his reaction is a look with an eye flash which could be interpreted as anything from giving the moron an epic Death Glare to going "Mmm... crackers!".
A lot of Grimlock's dialogue in "Call of the Primitives".
The Oracle: "Only you can save the world now, Grimlock."
Grimlock: "Me Grimlock feel important!"
Grimlock: [chuckles] "You are creator?"
Grimlock: "Grimlock laugh at little wimp who cause big trouble!"
Primacron: We are finished!! I've amplified the energy parameters, minimized the drivormenter, redirected the ion flow! I've tried EVERYTHING!
Grimlock: Me Grimlock solve problem! Wuh!
[Reaches over and pushes switch]
Primacron: Of course, the reverse switch! Why didn't I think of that?!
In "Five Faces of Darkness, Part 3", right after Wheelie shoots a Sweep in the face and he starts falling to his death:
Sweep: My guidance system is hit! Galvatron, save meeeEEE!
"Quest for Survival" had lots of hilarious moments with the Morphobots. First Starscream gets dumped on his ass by his own reflected blast, then Blaster uses rock music to drive them away, then during the battle Megatron gets thrown around by a Morphobot, and finally the Insecticon army getting annihilated by the Morphobots.
Minutes after Megatron has revealed himself to be Not Quite Dead to Ratchet, Ratchet starts with the snarkery. When he later asks how he came back to life, Megatron says he has every intention of telling him. Ratchet's response?
Dreadwind and Darkwing returning to Cybertron, having been certain they were chased by Mecannibals, and stating to Megatron that they're not really sure where their pursuers went. Cut to outside...
Mecannicabl: (feasting on a dead Cybertronian) Good food.
Mecannibal: And plenty of it!
Seconds after Grimlock's resurrection, he tries to rush Megatron. Megatron simply side-steps, and Grimlock falls through a hole in the wall, several stories up.
Seawatch's only moment of anything, when he drags Bludgeon around by the leg, and his wonderful line beforehand.
Seawatch: Hey, Bludgeon, you know how to ski? (starts dragging Bludgeon through the water) That's okay. Neither do I!
A Decepticon civil war kicks off with Shockwave levelling Scorponok's base, with a shot big enough and loud enough to be heard all the way across the other side of the Hudson (Scorponok's base is in New Jersey). The scene cuts to a bunch of New York office workers staring at the sight from a window, and someone says this.
Anytime the Autobots try to make sense of human customs; special mention goes to Bluestreak mistaking a kiss for some kind of "energy transfer," in Issue #11. Let's just say the comics make good use of the Fish out of Water situation the Autobots are in.