The scene where the Autobots and Decepticons engage in battle until their ships crash into Earth in "More Than Meets The Eye: Part One".
Megatron's first conflict with Starscream in "More Than Meets The Eye: Part Three". Megatron mocks his commander's plans to claim his position ("Mistake Number One!"), leading the furious Seeker to try and shoot him from behind. Megatron handily shields the laser and quickly puts the terrified Starscream back in his place:
Part 1 of "The Ultimate Doom" has Megatron pulling an epic Sadistic Choice on Optimus Prime. Either Optimus activates the final space bridge pylon, which would pull Cybertron into Earth's orbit and pretty much doom humanity and give Megatron a nearly endless supply of energy, or leave the pylon alone, which would destroy Cybertron and kill everyone on it. Optimus activates it, leading to:
Optimus: Have I saved Cybertron...only to destroy the Earth?
In "A Plague of Insecticons", Megatron tries to blow up an oil refinery by crashing a burning oil tanker into it. Optimus leaps into its path and capsizes the burning ship before it reaches the shore. Moments later Megatron is about to fire on the Autobots when Optimus rises from the water holding the entire tanker over his head like it weighs nothing. Then he does exactly what you think he's going to do with it.
Optimus Prime: Megatron...CATCH!
Omega Supreme gets one in the second-season intro to the cartoon. Blitzwing strafes the Dinobots and tries to take him on in a Tank Battle. Omega transforms... and steps off of Blitzwing as he turns to attack his next target.
In the episode "Changing Gears", Ratchet flying-jumpkicks Thundercracker right in the chest.
The end of "City of Steel", where Prime takes out Devastator with dialogue that would never be allowed in children's television these days:
Devastator: It will take more than your puny arm to stop DEVASTATOR!
Optimus: Right. Which is why it's lucky that the hand at the end of that arm... is holding a gun!
Starscream in "Atlantis, Arise!" Throughout the whole episode, he's suspected that the Sub-Atlanticans are planning to betray the Decepticons, and he is proven right when Nergill, the Sub-Atlantican king, has a ray built which can shut down Transformers. Later, Nergill is about to fire the ray at Grimlock and Megatron (knowing full well that the ray will deactivate both mechs) when Starscream snatches it from him and calls him traitor. In case you don't get what's so awesome about it: the Trope Namer for The Starscream actually saves his leader's life. Of course, he doesn't get any gratitude for it, but even so...
In that same episode, the Dinobots get one (yes, they are walking CMoAs, but still...). While the Autobots are at the mercy of the Decepticons and Sub-Atlanticans, the Dinobots are called in, proceed to smash through the Force Field erected over the battlefield, and smash the Decepticons. Grimlock then goes after Megatron himself, shrugging off several shots from Megatron's fusion cannon.
"The Key To Vector Sigma" has four that stand out.
Megatron gloats after revealing to the Autobots that the Stunticons have a combined form — Menasor. Then Optimus commands the Aerialbots to "show 'em what you've got!" Cue This Cannot Be! from Megatron as Superion, the first Autobot combiner, introduces himself.
Optimus Prime: Surprise, Megatron! Meet Superion!
The first-ever combiner-on-combiner battle, which of course starts with a great line from Superion before the mechs throw down.
Menasor: Menasor crush! Destroy!
Superion: Talk is cheap!
Just as Menasor is about to crush Superion, Omega Supreme returns and beats the ever-living scrap out of him.
Omega Supreme: Repairs complete. Omega Supreme!
Silverbolt overcoming his fear of heights just long enough to destroy the key, then losing control and saying his farewells as he spirals to Earth ("So long, cruel world!"), and then a Big Damn Heroes moment from Slingshot just before he hits the ground.
In "Starscream's Brigade", Megatron finally kicks Starscream out of the Decepticons after he tried to play, well, The Starscream one too many times. So what does Starscream do? He creates the Combaticons and comes within inches of defeating the entire Decepticon army, and actually makes Megatron surrender before the deus ex machina cuts his triumph short. Said deus ex machina is Menasor sneaking up on Bruticus and punching him so hard it makes a crater dwarfing Bruticus several times over (Bruticus is already the size of a skyscraper).
Megatron: It's no use! We must retreat! (He and his troops turn tail and run after trying to fight Bruticus and having him just No-Sell everything they hit him with.) Starscream: So, Megatron? Now, will you kindly tell the world who the new Decepticon leader is? Megatron: NEVER! Starscream: Bruticus? (Bruticus chases after Megatron and scoops him up, with Starscream looking on from a perch on Bruticus' shoulder) Megatron: Nooo! Starscream: Now, Megatron. Who is the new Decepticon leader? (Bruticus begins to crush Megatron) Megatron: Enough! Uhm...you are. Starscream: I can't hear you! Megatron: YOU ARE!
And then after Menasor deals with the problem, Megatron quickly reaffirms his position and gives Starscream an effective punishment:
Starscream: Bruticus?... (Megatron appears from the crater and grabs Starscream by the neck) Megatron: No, Starscream. Not Bruticus. It's Megatron, your LEADER! Starscream: Megatron, don't! PLEASE! Megatron: (grins evilly) This time it really is goodbye, Starscream. Astrotrain, get him and his giant ally off this planet. (cut to Starscream and the Combaticons stranded on a small crater in space) Megatron: You're banished from Earth, FOREVER! Starscream: You'll regret you did not destroy me, Megatron! I will have my revenge!
Pretty much any time the Autobots and Decepticons team up against a common threat was awesome, though a notable example is "The Core" where both groups fight to regain control of Devastator and stop the Earth's core detonating. It's probably this pragmatic reasoning from Megatron that sells it:
Megatron: I do this only for the benefit of my Decepticons. It grieves me to think you may also profit.
In "Enter the Nightbird", Megatron reveals his plans to replace Starscream. The usually-cowardly Seeker is so livid that he slugs Megatron in the face and requires an electric cage to be restrained. Then he later tops it by escaping and disabling Nightbird right as the Deceptions were about to win, saving the day for both himself and the Autobots by giving Megatron's new assistant a long rest—
Starscream: Looks like I'm just in time. Megatron's new assistant, huh? My Null-Ray will put her out of commission! (Emerges from his hiding spot and fires at Nightbird, immediately disabling her)
Megatron: (begins to pursue Starscream) Decepticons, after him!I WANT THAT TRAITOR'S STEEL HIDE!
Season 3 & "The Rebirth"
Blitzwing at the end of "Five Faces Of Darkness" saves the day, stands up against his psychotic leader and refuses to join the good guys, walking out of the series and into fanfiction forever.
Galvatron: You will never be welcome in the ranks of the Decepticons again! Blitzwing: Sometimes it's better to be known for one's enemies.
In Part 3, Wheelie declares "Galvatron is strong, but Wheelie is mean!" and shoots a Sweep in the face, killing him.
In Part 4, the Constructicons somehow converted a human city into Trypticon without the inhabitants noticing. Seeing Trypticon transform to robot mode as the citizens evacuate to avoid getting crushed is a thing of beauty.
A minor one comes for Wreck-Gar in "The Killing Jar" when he is abducted by the Quintesson scientist and placed in an immaculate room. Separated from the usual clutter of the planet of Junk, the Quint expects Wreck-Gar to have a breakdown. Instead, he simply tears strips off the wall until it's nice and junkified again.
Another is when the Quintesson scientist gloats over his prisoners in their cells. He zaps Marissa Faireborn with a "submission field" that pins her to the floor and enters her cell, intending to examine (read: dissect) her. Thinking quickly, Wreck-Gar fires a Rocket Punch through his bars that destroys the submission field's projector. The Quintesson barely has time to go Oh, Crap! before Marissa rises and beats him up.
Also, the Quintesson scientist lured Marissa onto his ship with a Hard Light projection of her father, Flint. When she catches on to the ruse, her "father" turns into a monster and attacks her, but she takes it out with a few punches and kicks.
"Dark Awakening" has Optimus Prime rising from the grave to scare off the Decepticons. "Decepticons! Leave this place, or DIE!" Later, Hot Rod — not Rodimus Prime, ''Hot Rod'' — manages to fight the zombified Optimus to a standstill until Optimus shakes off the Quintesson brainwashing. Followed by Optimus doing another Heroic Sacrifice. "Til all are one!"
"Nightmare Planet" has: Springer and Razorclaw forming an Enemy Mine to slay a dragon, giant!Galvatron versus giant!Rodimus Prime, and Daniel lucid dreaming and breaking free from the Quintessons' dream machine through sheer willpower.
Starscream successfully betraying Unicron in "Ghost in the Machine". Other than Galvatron shooting him down as he was escaping, it was a pretty badass moment.
Unicron: Now do my bidding. Complete the connection.
Starscream: (throws away the wires, laughing) Do it yourself!
"Webworld": The psychiatric-hospital-planet of Torkulon restrains Galvatron and tries to lobotomize him by invading and consuming his metaprocessor. What does Galvatron do? He invades Torkulon's mind by being just that powerful of mind and just that mad and proceeds to tear the place apart.
Galvatron: (quietly, while making the gun) I'll get this to work, and then I'll show them what they're dealing with. LET ME OUT OF HERE!
After ruining the entire planet:
Galvatron: This, Cyclonus, is beauty! Devastation wrought with precision and care!
It may seem like an empty boast at first, but Galvatron made good on his threat of "I will gut this entire planet"
A meta example for those Rooting for the Empire, this can also count as the Decepticons first on-screen victory that sticks.
And for the Autobots, Sludge managed to kick aside a Sweep and knock a berserk Galvatron into a rock face saving Ultra Magnus' life.
"Call of the Primitives": Grimlock defeats Tornedron, the younger brother of Unicron.
Grimlock: Grimlock saved universe! Grimlock hero!
The Predacons deciding they are Tired of Running and facing down Tornedron even though they cannot possibly win.
Headstrong: I detest fleeing. I would rather die fighting!
Razorclaw: He is right! Predacons, unite!
(The Predacons combine into Predaking.)
Predaking: Tornedron, face Predaking! To the end!
In "The Burden Hardest To Bear", a young kendo student manages to topple a Decepticon by slashing at his legs with a katana. Later, Hot Rod manages to defeat a Matrix of Leadership-empowered Scourge and reclaim the talisman.
After the Stunticons steal the Matrix from Rodimus and depower him back into Hot Rod, Galvatron puts the device into his cannon. His dreams of conquest... utterly fail when the ghosts of Primes past, including Optimus, appear like Hamlet's father and order him to "RETURN THE MATRIX!" It's like getting a look into how Galvatron sees the world all of the time.
"The Return of Optimus Prime" features the return of Optimus Prime. It also features something called a "Hate Plague" which is passed on by touch and drives the infected insane with hatred (mostly, people are also driven to infect others, and are just a little bit loopy when infected - Ultra Magnus cackles while chasing Rodimus, for example). Galvatron is scared witless by the plague (before infection). It's stated that it's spreading across the galaxy (and maybe the universe). By the end of Part 1, the only uninfected Transformers are Galvatron, Sky Lynx, an unnamed Quintesson and a small handful of Autobots (who were all wounded by a maddened Superion). Yep. No Ultra Magnus (one of the first infected). No Rodimus Prime (who spent half the episode eluding Ultra Magnus only to be infected by Wreck-Gar in a fraction of a second). Even the city-bots have been defeated or offlined. And the plague is still spreading. By the end of the story, only the reborn Optimus and the Quintesson are uninfected (and Optimus has special armour keeping him sane, he'd be maddened as well without the armour). Cue Optimus realising that wisdom beats hate... and unleashing the full power of the Matrix to the roaring tunes of "The Touch" by Stan Bush.
Wisdom beats hate. Prime saves the day. "The Touch" is played. It's frankly amazing. Especially if you're a little kid who watched as all the heroes and villains fell one by one.
Which is why many fans completely ignore "The Rebirth" episodes and consider this storyline the true grand finale of the original series.
Complete with the one thing you thought Galvatron would never say:
"There will be no war today, Optimus Prime, you have earned Galvatron's respect".
The following issue then has one of the most badass covers in comic history: Shockwave, walking alongside a wall with the words "[THE TRANSFORMERS] ARE ALL DEAD." written on it.
Shockwave and Megatron's fight in issue #6. Megatron starts it by shooting Shockwave at point-blank range. It doesn't kill the guy, but it does send him flying for at least a couple of miles. Then he gets right back up, and when Megatron arrives, uses a Sherlock Scan to figure out how to cripple Megatron in a few seconds.
The Dinobot's first appearance is one for them and for Ratchet, who'd made a deal with Megatron knowing he'd never keep it. So when Megatron makes his inevitable betrayal, Ratchet sics the Dinos on him. The Dinobots win.
Omega Supreme's introduction, curb-stomping several Decepticons, taking some of them out of the comic for years, and being badass enough to make Megatron flee.
From issue #12, Optimus Prime (who until then had been a captured disembodied head) returns to his body and gives a No-Holds-Barred Beatdown to the Decepticons.
The ending of issue #13. Megatron is about to kill the human that had been using him as a weapon against his will. However, said human states that he's not afraid of him due to taking a level in badass. Megatron is impressed enough to spare the guy's life.
Buster Witwicky manages to get a brief moment in one of the UK issues, when he takes the mech-suit Ratchet and Wheeljack had built for him and goes looking for a fight. He accidentally winds up fighting Shockwave, but manages to do something no-one else in the entire series does: Makes Shockwave freak out, just by triggering Shockwave's fear of burial. Not bad for a human.
From the UK comics, the introduction of the Wreckers, and their leader Impactor.
The moment when the Wreckers have decided that the war "isn't (their) fight" anymore, and are getting drunk in a bar. A Decepticon comes in and starts bullying one of the patrons. Twin Twist moves to intervene, but Roadbuster just says it's not their fight. This is the last straw for Twin Twist, who finally decides he's had enough, and takes the guy out in one punch, before turning back to the others.
Twin Twist: Not our fight? How can you say that? How can I say that? It is our fight. It must, always, be our fight. We're Autobots - and the responsibility comes with the job! How can we live with ourselves if we let Decepticon scum walk all over us? It's not too late, though... we have a chance— One chance— so...
The Wreckers: Let's do it!
After several issues of Galvatron remaining perfectly calm and unfazed by everything thrown at him, Jazz manages to finally get him angry by laughing at him. What made him laugh? The fact that just after Galvatron told him his origins, he finds out that Megatron is leading the Autobots, meaning it's now Megatron versus Megatron. Sure, Jazz pays hell for it, but still. It's the beginning of a very long case of Sanity Slippage for Galvatron.
The end of Target: 2006, where it turns out Unicron was well aware of what Galvatron was up to, and that he was the one who 'convinced' Hot Rod, Kup and Blurr to go back and stop him, effortlessly.
A moment from the UK comic series that doubles as a Crowning Moment of Funny. Rodimus Prime has a Decepticon in the exact same position that Optimus had Megatron in in the movie. The Decepticon asks for mercy, and Rodimus repeats Optimus's line "You who are without mercy, now plead for it?" However, instead of hesitating and being interrupted, Rodimus simply shoots the Decepticon in the face while yelling "REQUEST DENIED!"
From the UK comic: Ultra Magnus taking on Galvatron. Okay, yeah, he lost, but still.
Ratchet single-handedly sabotaging the newly returned Megatron's scheme, first by making sure a revived Starscream's personality would return, making him immediately surrender to whoever was attacking him, and second by using Megatron's own technology to bring back Jazz, Bumblebee and Grimlock.
Speaking of those three, their reactions to being revived is pretty good too. Do they stand around wondering where they are or what happened? Hell no. The first thing they do is go straight on the attack.
The Autobot Pretenders (Jazz, Bumblebee and Grimlock) and the Resuce Patrol Micromasters versus the Mayhem Attack Squad in #61 is made of awesome. Points go to Seawatch's line to Bludgeon.
Seawatch: Hey, Bludgeon? You know how to ski? (Starts dragging him through the water) That's okay. Neither do I!
Thunderwing's Dynamic Entry in issue #65, smashing through a wall. And Grimlock's utterly unfazed reaction is to instantly punch Thunderwing hard enough to send him flying. Thunderwing's reaction?
Thunderwing: Hnn. I almost felt that.
Scorponok and Shockwave's fight. It takes them all the way from New Jersey to the shores of Manhattan, still brawling all the while. Note that Scorponok spends most of his reign as Decepticon leader plagued by doubt, so Shockwave's really gone and pissed him off good.
The fact that Galvatron manages to con Primus. He puts it best.
Galvatron: For all their supposed "omniscience", even Gods can be tricked.
Then Primus brings the Autobots and Decepticons home in the blink of an eye.
In issue 79 ("The Last Autobot"), Fortress Maximus, the mighty but conflicted Autobot subcommander, vs. Galvatron, one of the most powerful single warriors ever forged, who dismantled pretty much every Autobot he'd ever fought, either barehanded or with his particle cannon. Recent events have driven Galvatron completely 'round the twist, and he has some lingering injuries, but he is still one of the most dangerous beings alive. Despite having part of his face torn off, despite being thrown around like a toy despite being physically more massive than Galvatron, and despite the Decepticon being so Ax-Crazy he rips out some of Fort Max's wires with his mouth, Max overcomes his mental weaknesses, and uses the fact that he is fairly bristling with weaponry to blast him, beat him down, and throw him into a freezing Arctic lake.
Fortress Maximus:We are Fortress Maximus, the Last Autobot, and you—you are history! *knocks Galvatron into a lake with an uppercut*
To further make it cool, the dizzying size of the cast of the comic meant that only the most well-known characters got more than one CMoA—even Optimus Prime only had three I can remember off the top of my head, and the final writer's favorite, Grimlock, only had a handful—so a severely underutilized character like Fort Max getting a Crowning Moment of Awesome is doubly cool.
Ratchet was a medic with laser scalpels as his main weapon, but was 2-0 against Megatron, for a while was the only functional Autobot in the early goings and saved the day with guts, determination and the inability to know when to quit. In some ways, he was more heroic than the Marvel version of Optimus Prime.
#58 and #59 are basically nothing but Ratchet being awesome.
Ratchet's Dying Moment of Awesome, beating the crap out of Starscream long enough to make sure the Ark crashes. Not awesome enough? This also kills Megatron and Shockwave in the process, not to mention seriously messing Galvatron up.
What was printed on the last issue's cover? "#80 in a four-issue limited series" It's not often a comic book series can have a Dying Moment of Awesome all its own, but this one did.
The last issue's got plenty of awesome. Such as the fact that even when everyone else has been killed, out of all the Autobots left, Kup is one of them. And he doesn't have a scratch on him.
Grimlock punching straight through Fangry's chest, like it's the most casual thing in the world, while at the same time lecturing Prowl.
Optimus' resurrection. And the fact that he's back in his original body.