Optimus Prime's defeat of Megatron in their fight at the end of "Darkness Rising", where Megatron learns that Optimus was buying time for the other Autobots to destroy the space bridge, that would bring millions of undead Cybertronians to Earth.
Megatron: Ah... Misdirection, Optimus. You would have made a fine Decepticon!
Optimus blocks Megatron's finishing strike
Optimus: I chose my side.
Optimus blasts Megatron point-blank
Bulkhead storming the Nemesis in "Darkness Rising". Heck, just about any time they decide to let Bulkhead cut loose will result in one of these.
3 words. Robot Friggin' zombies.
Optimus and Ratchet vs. Zombies. No contest.
Ratchet: "I recommend dissection..." *cue arm blades*
Bulkhead rips a Decepticon's spark out. It was just a mook, but that is awesome.
One for the guys behind the show and Starscream for actually being menacing during Fowler's interrogation.
Fowler not only surviving the interrogation (note, interrogation done by beings that don't care about human limitations) but getting some sarcasm in as well.
Bulkhead also gets one when Fowler attempts to put the kids in Federal Custody.
"WE'RE protecting them." *STOMP*
Masters and Students
Any time Skyquake (before he died and was raised as a zombie) is on screen.
Hell, even after that he still manages to be pretty badass.
One for Optimus:
"Skyquake, STAY DOWN. *punches Skyquake hard in the face*
When Starscream is using the Energon Harvester on Bulkhead, does Bulkhead die? No, he starts walking toward Starscream despite being overwhelmed, grabs the Harvester, punches Starscream in the face, and throws the unstable Harvester into the sky.
Bulkhead and Bumblebee's fight with Breakdown in the parking lot. Special mention goes to 'Bee landing a combo on the much larger Decepticon that ended with a flip kick and Bulkhead using a streetlight to whack Breakdown.
Optimus blindsiding an escaping Knock Out and running him off the road.
Arcee overcoming her fear of Airachnid and beating seven shades out of the rogue 'Con.
Jack blowing up Airachnid's ship with improvisation alone, something very few humans in the complete Transformers franchise have ever managed. Single-handedly, no less!
Out Of His Head
Optimus running through Starscream's heat ray in "Out of his Head".
And then causing an ungodly huge explosion.
Raf trying to stop Megatron (who was possessing Bumblebee at the time) from returning to his original body by leaping onto the cortical psychic patch, and Megatron's Villainous Rescue, in which he tackles Starscream and drags him away for punishment.
Bulkhead and Breakdown's Back-to-Back Badasses moment in episode 16, when they take on MECH together. Then, when Starscream and several Mooks show up, Bulkhead takes on all of them (including Breakdown) by himself.
Silas' Eviler Than Thou moment of kidnapping and torturing Breakdown was pretty awesome, when you consider how much Decepticons underestimate humankind.
Fowler's Big Damn Heroes moment in "Crisscross" (complete with attack helicopters), where he manages to scare off Airachnid.
For that matter, Airachnid and Arcee's rematch. Especially when Jack and Arcee manage to temporarily trap Airachnid in cement.
Gotta give Jack credit for swiping Silas' radio. Dude's big and surrounded by armed guards. That took guts.
In "Metal Attraction", there's the scene where Bulkhead and Arcee take advantage of being stuck together to perform a sneak attack on Airachnid.
Both Bulkhead and Arcee vs Breakdown and Airachnid fights qualify.
Arcee's own Big Damn Heroes moment when she catches Starscream off guard while he's threatening an immobile Bulkhead.
But Megatron gets a good one that episode, in which he's paralyzed and trapped under some rocks, only to find Jack drilling in an attempt to find Miko and Bulkhead. Does Megatron beg not to be killed? No, he actually goads Jack to do just that. Even when he's trapped, Megatron can still be intimidating.
Bumblebee punching out Airachnid while pretending to be immobilized in "Partners".
Starscream reverting some of his Villain Decay by nearly killing Arcee in a fight.
Arcee herself gets one when she has a Heroic Second Wind and beats the tar out of Starscream, scarring his face in the process.
One for the bad guys in Episode 22, specifically Megatron. Ratchet, hepped up on imperfect synthetic Energon, breaks into a Decepticon energon-mining operation, intending to take down Megatron. At first, Megatron merely laughs him off as the Autobot medic, then Ratchet punches him square in the face so hard that Megatron flies backwards into the wall. Megatron's response? To assess the damage, then deliver a Pre-Ass-Kicking One-Liner.
You've got to admit that when Ratchet punched Megatron in the face and sent him flying into a wall it looked damn cool. Even if he was doped up on robo-roids.
That whole first fight when Ratchet basically takes down a dozen Vehicons single-handedly also qualifies for similar reasons. Despite the robo-roids, it was one of the most awesome action sequences in the series to date.
And even after Megatron guts him, Ratchet is still able to fight Knock Out to a standstill.
June Darby chewing out the Autobots in "One Shall Rise, Part 1" for the way they've been putting children in harm's way. As someone who's always had a problem with children in war zones in many versions of Transformers, this Troper almost literally cheered.
Megatron calls up Unicron and offers to serve him. Unicron's response? To dismisses him as unworthy with an epic Reason You Suck Speech. He even makes Megatron resort to groveling.
Optimus when he meets Unicron for the first time. After Unicron attacks him, Optimus not only lowers his defenses, but tries to negotiate peace with the utmost politeness, even addressing him as "Lord Unicron." It doesn't work, of course, but you gotta give him some points in negotiating for mercy with the Cybertronian equivalent to the devil while being no less badass at it. And for a second it looks like it might work. At the least, Unicron has the class to actually stop and listen when Optimus shows deference and respect.
Megatron is inside the Autobot base during a temporary truce, and what happens? Raf confronts him, Jack refuses to be baited and Miko basically threatens to kick his ass if he betrays the 'Bots and has to be dragged away by Agent Fowler. The whole scene is one big ball of awesome.
Megatron holds off several giant mooks Unicron makes single-handedly, and actually kills three. The Autobots also get this in their Big Damn Heroes moment.
On a related note, Megatron punches one of the giant Unicron copies hard enough to destroy its head.
Soundwave dishing out a Curb Stomp Battle to Airachnid when she tries to take over the Decepticons and leave Megatron behind. The fight literally ends with the silent spymaster stomping on the traitorous Dark Action Girl, forcing her to yield.
Megatron being able to resist the power of Unicron is pretty darn awesome. Unicron ends having having to seize control of his body just to get him to do what he wants, and by that point it is too late.
Ratchet's retelling of the history of Optimus, Megatron, and Cybertron just felt so... epic.
It also gives Optimus's line, "I chose my side" so much more weight. He turned on his mentor figure in order to stand up for what he believed to be the way to save Cybertron.
Orion Pax Three Parter
A small bit, but I thought it was cool for Megatron to actually come up with a believable answer to Orion's question of why the "heroic" faction they belong to are called Decepticons.
As if we we needed more proof why Soundwave is awesome, he gets another one in "Orion Pax, Part 1". So, Arcee is on a rampage inside the Nemesis looking for Optimus/Orion, and is on a collision course with Soundwave while racing down a hallway in bike mode. Soundwave's response? Open a GroundBridge mere inches in front of him, just before Arcee runs over him. All while standing there silently. No movement. No speaking. It's like a study in badassery.
Arcee's rampage itself was still awesome. She manages to take down about ten Vehicons before Soundwave bridges her out.
Starscream is back, and he's making sure that the 'Cons feel it, also showing traits of being a Combat Pragmatist again. His Villain Decay is now being reverted further.
His escape wasn't bad either, defeating several air drones and killing the last one by blasting it several times at point blank range. Though admittedly he does get hit and sent crashing down towards the earth.
Bonus Points for taking down a jet-mode Vehicon with Jet-Judo!
The Autobot's raid on the space bridge, complete with Ratchet shushing a 'Con who tried to call for help.
Jack suits up and heads out to Cybertron. His salute to the others just before he leaves pretty well sums up his character development up to this point.
Major awesome points go to June for how well she's taking the whole thing.
Pretty much all of "Orion Pax, Part 3":
Orion Pax deletes the works of Project Iacon in an effort to deny Megatron the data for several Cybertronian WMD's. Megatron was smart enough to back up the data (itself an awesome moment for Megatron), but it's still a very establishing moment for Orion to uphold the same morals, even when facing almost certain death.
Later, when he whips out his guns when being kicked around by a pair of Vehicons and quickly kills them. Could count as a Funny Moment given the way he does it.
Heck, Jack himself got a moment when he absolutely destroys the rampaging Insecticon by throwing a Scraplet onto it and herding the entire swarm to chew it to rusted little bits. Note this is the same member of a species that knocked Arcee unconscious, not to mention seriously woundedMegatron in single combat later on, and Jack defeated it in one simple attack.
And that's after he faced it with nothing but a length of rebar. "Back off, bug!"
"Operation Bumblebee, Part 1" gives us Ratchet and Optimus gunning down an entire group of Vehicons while Bumblebee steals a MacGuffin right from Megatron's grasp. While inside a ground bridge!
Starscream strutting into MECH's base and basically telling them what they're doing wrong before proposing an alliance.
In "Operation Bumblebee, Part 2" we get a mode-locked Bumblebee, totally weaponless, charging in to battle MECH and Starscream head on alone. And he almost wins.
Bumblebee and Starscream's standoff also counts.
MECH finally gets fed up with their plans failing and takes Starscream's T-Cog when he narrowly fails.
Bulkhead grabbing the Forge of Solus Prime and promptly handing Breakdown his arse was pretty cool, then he goes on to do the same to Knock Out before Megatron intervenes.
To be fair to Knock Out, he did have Optimus and Arcee on the ropes with the shield generator and would have taken them down if not for Bulkhead's intervention.
Ratchet repairing Bumblebee's T-Cog. (Doubles as a heartwarming moment.)
In "Loose Cannons", Dreadwing and Wheeljack's second fight/chase is pretty cool, and it is stopped when Wheeljack and Bulkhead trap him at the end of a tunnel. Then Dreadwing detonates a bomb underneath Bulkhead's hiding position, burying Wheeljack underneath a thin layer of rock and then kidnapping Bulkhead.
The shootout between Dreadwing and Optimus is pretty epic, and Optimus finishes it by dropping a giant wrecking ball on top of his opponent.
To stop Dreadwing from blowing up Bulkhead with a bomb that's been clamped onto him, Optimus, Wheeljack and Bulkhead surround the downed 'Con. Completely undeterred by the fact that they could all be blown up there and then, they force Dreadwing to defuse the bomb.
Before that, Bulkhead breaks himself free and tries knocking Wheeljack out before running towards the sea, in an effort to stop his best friend being blown to scrap. Granted, the bomb was defused later anyway, but still.
Optimus Prime vs. Nemesis Prime in its entirety. Especially the end, where while Silas is distracted, Optimus gets his Heroic Second Wind and beats the scrap out of his Evil Knockoff, before dropping it through the roof and right on top of Silas. Ouch.
Agent Fowler -- who establishes himself as a retired Army Ranger -- infiltrating the MECH base, knocking out several Mooks along the way, then getting the drop on Silas and fighting him one on one. He loses that fight, yes, but he holds his own at first, and more importantly, distracts Silas from controlling Nemesis Prime long enough for Optimus to finish it off.
Agent Fowler also has the credential of being the first person to make Silas lose his cool.
On the villainous side, Silas using Nemesis Prime to defeat Bulkhead (easily the second strongest Autobot behind Optimus) in a little under 6 seconds.
The episode opens with Starscream stumbling into Bulkhead on the Nemesis. Bulkhead tries to get Starscream to show him the way out, but talks break down and Starscream slashes Bulkhead's chest, throwing Cliffjumper's death in his face in the process. Bulkhead then proceeds to beat Starscream to death. Only later do we learn that it's a clone.
Megatron is just wall-to-wall awesome here. He stalls the clones long enough for a break and kills three of them effortlessly, walks among an army of Insecticons like this is just a bad day at work instead of a major threat while gunning a few down, and throws out snappy one-liners all over the place.
Not to mention that he is perfectly calm when the Nemesis starts to crash land like it's, at most, a mild annoyance.
Bulkhead manages to stealth his way through the Nemesis, force it into a crash landing, then escape unseen.
Optimus and Bumblebee's battle with the Insecticons.
Arcee and Airachnid's fight, which ends with Airachnid being sealed inside a stasis pod.
Starscream's clone attack had one high point before it all went downhill. When Megatron goes to the bridge to confront him, he realizes every single Vehicon on the bridge has been brutally murdered.
Starscream offing his treacherous clone with two brutal close-range missile shots. While aware of the pain it would cause.
After Knockout comes out of stasis, with Jack right in front of him, we get this:
Knockout: *Points his drill at Jack* Say "Ahhh..."
Made especially awesome by the fact that the other Autobots were more than capable of helping out, since they had been taken out of stasis already. Ratchet personally went to retrieve Jack because it's Jack.
Jack climbed Megatron to get to the fuel dump control. Lemme repeat that: Jack. Climbed.Megatron. I guess going to another planet to save your own really does something to a person.
Then he repeats it by climbing Knock Out to grab the data chip. When the Decepticons were explicitly reviving from stasis at the time. Megatron, at least, was quite neutralized at the time. Knock Out woke up and nearly caught him. He risked being left behind to retrieve the Iacon data.
"Shock and Drop". To clarify, Arcee gets the Insecticon to short-circuit by getting it to step on the electricity wire.
And before that, Knock Out shocking the scrap out of Arcee during their one-on-one fight.
Vogel ramming Knock Out with his train. Twice.
Beforehand, Arcee forcing a train line to change to another point, with literally a second to spare before it crashes.
I'm giving one to the writers of the series for actually having Miko not only be somewhat useful, but have her exclaim about feeling left behind by Jack and not come across as annoying and whiny was pretty good.
Dreadwing's fight with Optimus. It takes a real Badass to go toe to toe with Optimus Prime and live, something only Megatron has done up until now.
Optimus shooting at a cliff face and causing an avalanche to fall on top of Dreadwing. Dreadwing was lucky to have survived that.
Starscream got a real moment when he obtained the Apex Armor and took on both Optimus and Dreadwing, forcing them to work together and use cunning to defeat him. Yeah, he lost, but he still walked away (literally) with the armor. Looks like Screamer's time as an Ineffectual Sympathetic Villain is just about over.
Optimus and Dreadwing teaming up to defeat the Apex Armor-wielding Starscream.
The whole fight between Soundwave and Wheeljack was awesome. Wheeljack actually landed a few hits and cracked Soundwave's visor, but then Soundwave lured Wheeljack down to where the relic was and when Wheeljack thought that Soundwave was down, the spymaster grabbed the relic with one of his tentacles and used it to defeat Wheeljack.
Don't forget that Wheeljack actually tackled Soundwave off the side of the cliff.
Ratchet and Raf manage to upload a virus into Laserbeak (who finally got named in this episode) and plant a bomb in the deployer to act as a decoy so that the virus goes undetected. What does the virus do? It downloads the entire Iacon Database from the Nemesis to the Autobot base!
Bulkhead's way of dealing with the relic he was after. Even though he's severely weakened by the relic and facing three Insecticons, he was able to take all three out and he destroyed the relic, because if Megatron had it, it would be worse for everyone.
Doubly awesome because he uses the Tox-En as a weapon against Hardshell and his goons.
Even before that Bulkhead leading an Energon trail away from the volcano, to buy him more time. Surprisingly strategic.
Hardshell gets Bulkhead back though. Literally. After getting thrown into the volcano with the Tox-En, he climbs out and shoots Bulkhead in the back with a missile.
An out-of-universe one which goes more to the show. Transformers: Prime was the first Transformers show to get nominated for the Daytime Emmys after Beast Wars (which came out fifteen years before). It was nominated for six awards, and ultimately won two (both were for Outstanding individual achievement in animation).