A Dog Named "Dog": Predaking doesn't have a real name, other "the predacon," until he transforms and names himself.
Aborted Arc: Subverted. After "Stronger, Faster", the Synth-En ends up in the hands of the Decepticons, and then it's never brought up again... Until Season 3, where the Synth-En finally makes a reappearance in "Thirst" and plays a pivotal role in Cybertron's revival.
Starscream strongly implied he would mount a future, far more competent coup on Megatron after Breakdown is rescued from MECH, and flat-out tells Breakdown he should choose to side with him once the time comes. However, Breakdown is suddenly killed by Arachnid early into season two, and even before that, Starscream abandoned the Decepticons, so a possible Subversion.
Breakdown and Bulkhead's rivalry was continuously hinted at several times during the first season, with the latter swearing Breakdown's past actions were unforgivable. The two's history was never revealed, as Breakdown was killed by Arachnid, and Bulkhead didn't even learn of it for several months, and even when he did, he reacted more to Silas now being in Breakdown's body more than anything.
The Nemesis cryptically hangs up when Ratchet asks why it is gathering the Iacon relics, but nothing more is made of the scene ever again.
In-universe: Megatron had grand plans for an army of Predacons to unleash on humanity, but when he discovered Predaking's sentience, he realized how quickly they could turn on and overpower him and orders them exterminated.
Another in-universe example: A dying Optimus believes Smokescreen is worthy to become the next Prime, but Smokescreen refuses and restores Optimus. This is only brought up two more times, the latter occasion just trying to smooth it over with the scene feeling like the show saying, "Nope, sorry, he's not gonna be a Prime, move along, please."
Airachnid's final appearance in the series has her contracting vampirism and spreading it amongst her newly regained army, and on one of Cybertron's moons. This is never talked about again.
Acting Unnatural: Miko and Raf trying to lie to Optimus in "Speed Metal." Optimus is not convinced.
Action Girl: Arcee. Miko graduates to this by the end of the series.
Adaptational Badass: Taking a cue from the live-action films, Bumblebee and Starscream are quite competent soldiers. 'Bee isn't quite the bruiser that his movie counterpart is, but he charges headlong into a fight and holds his own just as well. Starscream is also scary in both his competence and appearance; they made him a sadist who is unafraid of killing prisoners for talking back at him and willing to make cheap shots to gain the advantage in a fight.
Wheeljack in Generation One was a mad scientist, inventing many wacky devices that, more than often, ended up exploding. In this show, he is a dual-sword-wielding ex-Wrecker who is willing to go up against a 'Con army and boast about his odds. Unlike his G1 counterpart, this Wheeljack invents things on the fly (Yes, he's MacGyver) and for being an explosives expert.
Breakdown, considering most of his previous incarnations are critically paranoid nutcases. Here, he's a tough bruiser who's the rival to Bulkhead.
In the War For Cybertron game, which is part of the same continuity, he used to be a critically paranoid nutcase (though still useful in battle) in this universe as well, so with him, it's also a case of Took a Level in Badass.
Ultra Magnus as well. He most certainly can deal with you now.
Adoring the Pests: In the episode "Scrapheap", Raf finds a small, adorable robotic creature the size of a kitten, called a Scraplet, and assumes it is the Autobots' pet. It turns out Scraplets eat metal, especially living metal, like, say, the Autobots...
Adult Fear: June Darby worries about Jack riding and racing Arcee because she works in an emergency room. Naturally, she's also not at all pleased after realizing that children are near the front lines of five robots' war against the Decepticons. Her fear comes true at the end of the Season 2 finale, as she has no way of knowing where the kids are.
Another example comes when MECH kidnap June to get at Jack and Arcee. Sylus finds out about June because of Jack's social network page. This kind of thing is a very real threat regarding sites like Facebook.
Soundwave pulls this with a Ground Bridge on Apex Armored Miko in "Deadlock". This then turns into Hoist by His Own Petard when Raf opens a Ground Bridge behind Soundwave, thus banishing him into the Shadowzone.
Alas, Poor Villain: While Skyquake was done in by his own refusal to let bygones be bygones, Optimus muttering how he didn't want to have him killed is rather sad. He's also now condemned to spend eternity in the Shadowzone dimension as a mindless zombie unless somebody comes to put him out of his misery, which is pretty unlikely.
Alien Autopsy: What MECH does when they capture a Cybertronian. They work pretty fast and usually do their autopsy in the field. They don't really care if it's an Autobot, a Decepticon, or a rogue Cybertronian; dead or alive, just as long as they have one to study.
On the other side, this is what Knock Out ends up doing to Silas at the end of "The Human Factor". Oh, the irony.
Optimus Prime's realization of MECH's intentions inverts this (technically, for him, we are the aliens). He explicitly compares MECH to the Decepticons.
Debatable with Unicron. While he originates from Cybertron and is, undoubtedly, the Chaos Bringer, his status as an "alien" comes into question when, in "One Shall Rise, Part 1", he's revealed to be the core of the Earth.
Aliens Speaking English: Justified by the fact that the Cybertronians have been on Earth some time prior to the start of the series, they have accessed the wireless networks around the world, and learned several languages but only speak English as it appears universal.
All Deaths Final: As stated by Word of God, but not consistently upheld. Bumblebee, Optimus, and Megatron are all brought back from the dead, and Optimus's permanent death only comes in the final minutes of the series.
Played straighter at the end of "Darkest Hour", when the Decepticons launch a full-scale attack on the base, culminating with the Nemesis completely obliterating the mountain, after which Starscream and Megatron land in the wreckage and gloat over the Autobots' defeat. The Decepticons don't get much time to gloat, though: their new fortress, Darkmount, is captured and destroyed at the end of "Rebellion."
A Million Is a Statistic: What makes Optimus decide that enough is enough and Megatron needs to die? Was it starting the war that destroyed Cybertron? Was it the development of bioweapons? Was it spreading the war to other planets? No. It was almost killing Raf.
Anachronic Order: Four episodes back to back in the second season ("Tunnel Vision," "Triage," "Triangulation" and "Toxicity") all occur simultaneously, unified by a race to gather four different Iacon artifacts by four different groups of characters. Each episode largely stands alone but drops hints towards what is happening with the other characters. "Toxicity" makes an effort to connect the episodes together and bring the Story Arc to a close.
Ancient Astronauts: Played with - Despite Cybertronians knowing about and visiting Earth for a very long time, the actual impact on life here has been minimal until the events of the show itself. To wit: Shockwave's early Predacon experiments (or their remains, at least) were the inspiration for the monsters of classical mythology, but that's the only straight example. There was at least one battle on Earth that no human seems to have witnessed and ancient Cybertronians would occasionally appropriate local art to place coded signposts for future visitors. Neither of these made any impact for human civilization other than that one statue in a museum. The fact that Unicron is the Earth's core had no influence on the development of life on Earth. He considers us all parasites feeding on his body and need to be destroyed.
And I Must Scream: Being trapped in a stasis pod. The Immobilizer seems like it would also count, given the extremely detailed account of its effects Bumblebee gives to Predaking.
Soundwave's final fate is to be trapped in the shadowzone for all eternity by Raf catching him between two groundbridges.
Unicron didn't sound very happy about being trapped in the Allspark reliquary.
...And That Little Girl Was Me: In "Operation Bumblebee, Part 1", Ratchet tells Raf how the field medic who saved Bumblebee after Megatron had tortured him wasn't able to fix Bumblebee's voice box. He was speaking about his own inability to completely fix Bumblebee since he was that field medic. Raf says that its a good thing the medic was able to save Bumblebee.
Ratchet: Yes, well... the medic could have done better.
And This Is For...: When Arcee first battles the Vehicons, she begins pummeling one of them whilst exclaiming; "This! Is! For! Cliff!"
Animation Bump: Comparing individual episodes, it's obvious that they were truly fine-tuning the animation while season 1 marched on. This is especially obvious in the season one finale, where the mouth animations - best described as "adequate" before - become much more accurate.
It's particularly evident in "Partners", but the lighting and the detail on the individual characters (dings, scrapes, paint scratches, etc.) has only improved as the series progressed.
Knock Out: Even if I had helped him to seize this ship, he probably would have just fired me out of the first airlock. [beat] Oh, and he's rude.
Amusingly enough, he actually seemed more bothered by the jaywalking part. Presumably as a Decepticon, betrayals like that were practically expected, but when Starscream angrily yells at him to shut up during a stand off with the Autobots, he looks visibly hurt (likely due to their Villainous Friendship).
Art Evolution: War For Cybertron was, more or less, a blending of the design aesthetics of the original G1 series with the live-action films, leaning slightly more towards the former (blocky proportions with a lot of moving parts). The design for this series has been described, more or less, as being a more evenly balanced mix of the style of Transformers Animated with the films, leaning a little more towards the latter (complex looking designs with sleek proportions).
Several episodes in, people were already commenting on the show improving in art style from the first episode, particularly the look of the environments.
In "Orion Pax, Part 1," the interior of the fast food takeout stand Jack works in now looks fully functional, unlike in the first episode where it looked unusually empty.
Generally in the first season the vast majority of action scenes took place in desert canyons, arctic locales, or underground caves, with a scattering of scenes in the Nemesis hallways or in open forests. It was probably due to cost and a tight timetable. The second season immediately started adding new locales like open prairies, mountain roads, cliff faces, shipping yards and Cybertron itself.
Art Shift: Any time a character tells a brief story about some event in Cybertron's past, the accompanying visuals look like a Limited Animation of a comic book. It started when Optimus told the story of the Transformers and the war to the human kids in the first episode, but also used when describing the war between Primus and Unicron and the Thirteen Original Primes, explaining Optimus and Megatron's history before the war started, when describing how Bumblebee lost his voicebox, Bulkhead ominously talking about the danger of Tox-En and when showing Smokescreen's backstory.
Likewise, when Optimus describes what would happen to Earth should Megatron bring an undead army to it, various elements of the scene are non-CGI elements such as the fire and explosions.
A Taste of Their Own Medicine: When Breakdown is at MECH's mercy, the first thing Silas does is core out his right eye. In "Thirst", we see that part of Knock Out's torture involved blinding Silas in his right eye.
Badass Bookworm: Ratchet and Smokescreen for the Autobots, Soundwave and Shockwave for the Decepticons. Raf gets into this from time to time as well.
Optimus may count as the ultimate Badass Bookworm. Remember, the guy used to be an archivist, and ended up as the guy who, had Megatron not begun the civil war, would have been the leader of the entire PLANET. Strictly speaking, Optimus is basically the rightful ruler of Cybertron due to his elevation to Prime first by the council and then later by being given the Matrix by Primus himself. How many bookworms can make that claim?
Badass Bystander: The human kids can't really get involved with the heavy metal action, but the show has gone out of its way to show moments where they are able to help just by being an extra set of hands.
Badass Normal: Agent William Fowler. He "has some pretty big bearings, for a human," according to Bulkhead. He's willing to argue with the Autobots, dogfights Soundwave's drone in a helicopter rather than be captured without a fight, and continued to mock Starscream while being tortured, never giving up the location of the Autobot base.
His Badassitude is further shown and justified in "Nemesis Prime". Turns out he's a retired Army Ranger.
Apparently, he has also "trained in Covert Ops".
Jack gets into this every now and again. Raf proves to be helpful with his tech savvy. Miko wants to be this, but is too enthusiastic to be of actual help, at least at first. Later on, she kills Hardshell with a pair of missiles from the Jackhammer and drives off Starscream and his troops with the Apex Armor.
The human kids get a huge moment in the finale when Jack and Miko ground bridge to the bridge of Nemesis, with Miko in the Apex Armor and take down Soundwave himself. How? By using Soundwave's strategy of relocating attackers with ground bridge technology against him and sending him to the Shadowzone.
Bad Boss: A common trait among whoever's in charge of the Decepticons, or at least a squadron of Vehicons.
The Bad Guy Wins: "Darkest Hour", full stop. Cybertron remains a wasteland; Megatron has constructed a new fortress on Earth, right over Jasper; Team Prime and the kids are scattered to the four winds; June thinks her son is dead; the Autobase is destroyed; the Decepticons have begun an outright invasion of Earth to claim it for their own; and Optimus Prime is mortally wounded and trapped inside the Autobot base because he was destroying the Base Ground/Space Bridge to prevent his team from being followed when it blew up.
Bad Liar: Miko, Raf, and Bulkhead. It's a minor miracle the kids haven't blown their cover with their parents.
Followed up by an epic Call Back in "Orion Pax, Part 3", with the striking and blocking positions reversed. Could also count as a Bookends situation, since it effectively closes a storyline lasting seven episodes.
Bare Your Midriff: Quite a few of the Transformers give the impression of bare middles and abs.
Barred from the Afterlife: Unicron explains to a confused Megatron that the reason his Spark had not become one with the All Spark was due to the Dark Energon tainting his Spark, which instead drew him to Unicron's anti-Spark. Unicron's explanation seems to indicate this is permanent. Whether Unicron's imprisonment changed that is left up in the air.
Bash Brothers: Knock Out and Breakdown. Bulkhead and Wheeljack were this back on Cybertron as part of the Wreckers.
Batman Gambit: Ratchet decides that losing one Iacon relic would be worth it if he could use Laserbeak to download the entire archive from the Nemesis so the Autobots could find the rest of the relics before the Decepticons could. He also uses one of Wheeljack's grenades as a decoy Booby Trap in order to throw off the 'Cons from their true plan.
Battle Couple: Miko muses to herself about Bulkhead and Arcee being one in "Metal Attraction", though she later becomes distressed when it appears to be becoming literal.
Battle in the Center of the Mind: Subverted in "Sick Mind". Megatron tries this, but any attacks he throws at Bumblebee are useless. The two are forced to an impasse.
Belated Love Epiphany: In a platonic way, Arcee doesn't realize that she cared for Cliffjumper until this latter is killed by Starscream.
While they were shown as friends, Knockout didn't show any emotion when Breakdown died, until this latter is revived and possessed by Silas. When they face again, Knockout is upset and begs Megatron to let him avenge Breakdown.
After all his treachery and backstabbing behavior,Starscream seems genuinely upset when Megatron dies in Deadlock episode.
In Deadlock when Bumblebee is blasted by Megatron, Optimus goes berserk and unleashes probably the most vicious beating he's ever delivered on Megs.
Beware the Quiet Ones: In "One Shall Rise, Part 3", Soundwave utterly wipes the floor with Airachnid for trying to usurp Megatron's position. Knock Out then quotes this trope, nearly word for word. It's implied in the lore that Soundwave is one of the few beings that can stand toe-to-toe with Megatron, being also a gladiator in Kaon with him. The only other Bot so far to be able to do this is none other than Prime himself.
BFS: The Star Saber, the signature weapon one of the original Primes, Prima. While it was normal sized for Prima, those original Cybertronians were explicitly much larger than the average modern Cybertronian. Thus when you see Optimus with it the thing is about as tall as he is. Not to be outdone, Megatron uses the Forge of Solus Prime to create an Evil Knockoff.
Big Bad Ensemble: Different antagonists are focused upon on an episodic or arc-to-arc basis. Megatron and his Decepticon army are the chief bad guys of the series, but other enemies include Silas, Airachnid, and Starscream.
Big Damn Heroes: Happens a lot. The most notable examples would be Wheeljack showing up to join the battle to buy the Autobots time to evacuate their base when the Decepticons finally find it, Optimus Prime returning in a new, upgraded form and single-handedly turning the tide in the battle over Darkmount, and Bumblebee coming back from the dead to save Optimus by driving the Star Saber through Megatron's spark.
Big Guy Fatality Syndrome: Excluding the mooks, the occupation of being the resident Big Guy or Brute is the most hazardous on the show. All of the Decepticon heavy hitters bar Predaking die note Skyquake, Breakdown, Dreadwing and Hardshell. Of the two Big Guys on the Autobot team, Cliffjumper dies and Bulkhead is badly damaged during "Toxicity," and doesn't return to field duty for several episodes.
Big "NO!": Quite a few of them through the series.
Bittersweet Ending: The ending of Season One. The Autobots stop Unicron from awakening and the Earth is saved. However, Optimus loses his memories of the Autobot-Decepticon war, and Megatron uses this to get him onboard the Nemesis and away from Autobot hands.
The endings of both "Triage" and "Toxicity" could be considered this, even if Bulkhead doesn't die.
The conclusion of "Inside Job" leans more towards a Downer Endingsince Starscream returns to the Decepticons with all four Omega Keys. Though there is some solace in the fact that Smokescreen did manage to escape from the Nemesis.
The end of the series. Both factions get what they ultimately set out to achieve (the end of the caste system, the end of the age of Primes, the revival of their homeworld), if not everything they wanted, and thus, everyone wins. Even Megatron decides that enough is enough. It comes at the cost of Optimus performing a Heroic Sacrifice to restore life to the Well.
Bizarre Alien Biology: The fact that they're robots who use the term "biology" to refer to their structure and talk about stuff "flowing through their veins" should clue you in that these are neither life nor robots as we know them.
Blatant Lies: Megatron assuring Fowler via radio communication that now that the Autobots have been defeated and the Decepticons have constructed New Kaon/Darkmount, all they really want to do is live in on Earth in peaceful coexistence with humanity, with whom they have no quarrel. Fortunately, Fowler's not an idiot so he doesn't buy it for one second, though it still nets a complement from Starscream.
Blofeld Ploy: Starscream does this in "Deus ex Machina". When Knock Out tries to claim credit for retrieving the Energon Harvester, Starscream aims it in his direction and fires... killing a hapless Vehicon positioned behind them.
Bloodless Carnage: Breakdown's remains are completely devoid of Energon, which stands in odd contrast to the fact that Starscream, Airachnid, and Megatron all bleed copiously from (non-fatal) wounds in the exact same episode. Vehicons and Insecticons don't seem to bleed much, either. Case in point: Megatron ripping Airachnid's Insecticon's forelegs off before decapitating it, with nary a drop of Energon to be seen.
Starscream didn't leak much Energon either when he lost his arm in "Shadowzone", while he bled copiously from less serious wounds in "Orion Pax, Part 2" and "Crossfire."
Blood Sport: Ratchet considers monster truck rallies to be this.
Which takes on a slightly darker dimension when we find out that Cybertron had actual gladiators and Megatron used to be one.
Book Ends: "Partners" opens with Starscream monologing about how he's accepted his position as Megatron's servant. It ends with Starscream monologing about how he has no place on either side.
The "One Shall Fall/One Shall Rise/Orion Pax" Story Arc is effectively bookended by fights between Optimus and Megatron wherein one pulls a Barehanded Blade Block on the other.
The arc from "Darkest Hour" to "Rebellion" is marked by the capture and destruction of a base for each side, Outpost Omega One for the Autobots and Darkmount/New Kaon for the Decepticons.
The opening shot of the series is a couple of birds flying into the sky. The series finale proper, "Deadlock", has the same number of birds flying in the same way at the beginning of the epilogue with the Autobots' farewells to the humans and Earth.
The series itself begins and ends with a multi-part mini-arc regarding the use of Dark Energon to raise an army of undead Cybertronians. The arcs are even title swaps of each other: Darkness Rising, Predacons Rising.
A Boy and His X: Threefold. The creators have even admitted that they wanted the humans' relationship with the robots to resemble the close dynamic seen in The Iron Giant.
Brain Uploading: Optimus Prime loses his memories after using the Matrix to defeat Unicron and reverts back to his original pre-prime personality, Orion Pax. It falls to Jack to restore Prime using the Key to Vector Sigma.
Later, Soundwave deletes his own hard drives to prevent information from falling into Autobot hands. However, he is fully restored by Laserbeak when the drone finds him and reconnects.
Break the Cutie: After Bulkhead is nearly killed, Miko finds out revenge is not all it's cracked up to be.
Brick Joke: When Smokescreen dove off of the Decepticon warship, Megatron threw 2 Vehicons after him, one of which turns out to be a car-based Vehicon. Later, after Smokescreen phases through the ground causing several pursuers to crash into it behind him, the unfortunate car-based Vehicon smashes into the ground a moment later.
In an interesting turn of events Hasbro was insistent on keeping the continuity vague on the matter to allow full freedom between the different productions. But during production of Transformers: Fall of Cybertron High Moon Studio has said they were working on bridging the story gap between the two much better.
Broken Faceplate: Inflicted on Soundwave by Wheeljack in "Triage", and yet he ignores it and keep on fighting, even though the Wheeljack just put a crack in his face. It just makes him that much more badass.
Broken Masquerade: The appearance of a massive Decepticon fortress within driving distance of metropolitan area surely qualifies, barring a truly epic coverup. This wouldn't be the first time such a spectacle was dismissed by the human population.
Some of Fowler's dialogue with his superiors in early season three implies that either The Masquerade is still holding, or the government would like to think so at least.
Bullying a Dragon: Starscream's initial treatment of Predaking provides an almost literal example of this, with him insulting and striking the beast despite the creature being much larger and stronger than he is. This all stops when the Predacon demonstrates the ability to speak and transform...if only because Predaking makes it clear what will happen if it doesn't.
Came Back Wrong: Dark Energon revives the dead, but turns them into mindless berserkers unless something is around to command them, at which point they become his mindless berserkers. ("His," in this case, meaning Megatron's once he jammed a shard of Dark Energon into his slaggin' spark chamber.)
Bulkhead mentions Perceptor's Paradox during his scientific rambling in "T.M.I.".
Wheeljack also mentions fellow Wreckers Seaspray, Roadbuster, Pyro, Impactor and Rotorstorm during "Loose Cannons".
Smokescreen name drops the Constructicons (along with Alpha Trion and Halogen) in his debut episode.
Call Back: When Fowler finds the kids at the Autobot base in "Darkness Rising, Part 3", Jack says they're interning for a science scholarship. When Fowler meets Jack's mom at the end of "Crisscross", Fowler tells her Jack's his intern. (Jack then tells him not to bother; she already knows the truth.)
Ratchet tells Bulkhead that he needed the tool that the latter had just crushed in the premier of Season 1. Bulkhead smashes a similar tool in the Season 2 premiere and asks "What? You needed that?!" The line makes another appearance after Optimus Prime destroys the Omega Lock to save Earth from cyberforming. And while Ratchet was captured, Raf filled in for him as the resident techie, complete with a "Miko! I needed that!"
Knock Out gets one mixed with a Dark Reprise when he taunts Silas/Cylas moments before dissecting the latter, especially about Breakdown's missing eye.
Car Fu: Very common, thanks to the characters' need to keep their presence a secret. But it's not restricted to covert battles either - it's clear that part of training to be a Cybertronian warrior is to know how to run your enemy off the road.
Cassandra Truth: In "Crisscross", Jack tells his mother exactly what the deal is with him and his motorcycle. An uncooperative Arcee ensures that she doesn't believe him. Later on in the episode, when said mother is kidnapped by Airachnid and Jack and Arcee come to the rescue, Jack says he can explain everything, before stopping and going, "Wait, I already did."
Agent Fowler has a similar problem when debriefing his superiors after the incident with Nemesis Prime. Until Optimus Prime showed up in person to prove that he was alive and well, Fowler's superior was ready to send him away for psychiatric rehabilitation.
Casual Danger Dialog: Fowler reacts very nonchalantly to being tortured, though it's mostly so he can mock Starscream. In the end, the torture leaves him so drained that he's delirious and saying how much he likes pie.
Fowler often makes a patriotic reference like "You can eat my star spangled shorts!" or "Well, I'll be a bald eagle!" In "Stronger, Faster",
Ratchet: "I needed that!" any time his equipment gets broken.
Miko has "Suh-weet!"
In "Stronger, Faster", under the influence of Synth-En, Ratchet makes a temporary one for himself - "Hooah!" It's hilarious to hear a 'bot who must be the human equivalent of about 60 jump into battle like that.
Knock Out has a habit of telling anyone who damages his paint job "You scratch my [blank], I'll scratch yours." Obviously he doesn't mean this in the nice way.
Not exactly a catch phrase, but Optimus sure does say "It would stand to reason..." alot, followed by him spouting off something insightful.
Cell Phones Are Useless: "Shadowzone" gets a bit schizophrenic with this trope. While stranded in another dimension, the kids try to use Miko's cell phone to call for help, but she left it at the base. Then, Jack realizes he still has his and uses that. The call gets through, but since they're in a freaking alternate dimension, the call is unintelligible. Then the kids realize they can get around this problem with texting. It works. Possibly justified, if the dimensional shift introduces heavy interference, but still lets some of the signal through. Text, which is is much smaller in terms of the amount of data that needs to get transmitted (as well as simpler and easier error-correction), could legitimately get through where voice cannot.
Chekhov's Armoury: "Regeneration" sees the Autobots finally making use of every single one of the Iacon Relics they've collected. And it is epic.
Chekhov's Gag: Bulkhead breaks a piece of Rachet's equipment as a demonstration to Agent Fowler about how the Autobots use precision force, with Ratchet audibly annoyed by him. That same random machine is turned into a chaotic spider-like drone by Dark Energon.
Wheeljack's grenade. Makeshift's disguise as him includes one, which winds up being used to kill him.
The camera on Miko's cell phone comes in handy on multiple occasions.
Played with in "Predatory". Jack mentions his pocket knife and fire starter at the beginning of the episode, setting up two guns. When Jack is being chased by Airachnid, he takes out his knife, says "Who am I kidding?" and keeps running. The fire starter, on the other hand...
The Dark Energon shard Starscream plucked out of Megatron in an attempt to murder him is used by Starscream to empower himself.
The Harbinger. The downed ship becomes Starscream's base of operations in Season 2. It reappears again in season 3 as the Autobot base for the attack on Darkmount, and is presumably the source of much of the Cybertronian tech used in Hangar E.
The piece of the Decepticon's ship Bulkhead rips off while protecting Miko turns out to be very important the next episode.
Optimus tries using the Spark Extractor the Autobots captured in "Operation Bumblebee, Part 1" against the Decepticons. He fails.
The photo that Soundwave manages to get of the kids during the five-part pilot makes a return at the end of "The Human Factor."
"Alpha/Omega" is rife with these: The Decepticon Spacebridge, Forge of Solus Prime, Megatron's Dark Energon cache, and the Phase Shifter all make reapperances in quick succession.
The Star Saber spends most of season 3 locked away in the Decepticon Warship. Smokescreen springs it in "Deadlock", and Bumblebee uses it to kill Megatron.
Raf uses the Shadowzone from way back in season 1 to dispose of Soundwave in the series finale.
The Well of All Sparks is given cursory mention only once in "One Shall Rise, Part 1", while discussing the history of Unicron. It's here that the Autobots eventually fire the rebuilt Omega Lock into Cybertron's core, rendering the planet sustainable once more.
Chekhov's Gunman: A nasty example in the form of several deceased characters' corpses. If the body hasn't been utterly destroyed, you'll likely be seeing them again.
Cliffjumper is the first and best example: though he died so early in, the event has long term emotional consequences for the team (particularly Arcee) and his corpse is Megatron's first Dark Energon test subject.
Skyquake is killed off almost immediately, but his death and subsequent resurrection become major plot points with the emergence of Dreadwing.
Breakdown's remains are stolen by MECH and patched back together as a body for the critically injured Silas.
Starscream's last clone is killed at the end of "Armada," gets his T-Cog harvested in "Triangulation," and makes a final reappearance in "Inside Job" when Starscream uses his corpse to distract the Autobots so he can steal the Omega Keys.
Upon viewing Hardshell 's corpse as proof that humans are more dangerous than he initially thought, Megatron begins taking an interest in the Autobots' allies. This would have critical consequences in the Season 2 finale.
Finally subverted with Dreadwing.
Cliffhanger: Several during season 1, especially the last 4 episodes.
And then there is "Triage" and "Toxicity", which uses the same cliffhanger twice, but somehow making it work both times.
The end of "Regeneration": The Autobots have managed to activate the Omega Lock, thus eliminating the whole "political influence" issue, only for Megs and friends to show up toting cylinders with the kids trapped in them. So Optimus is given an ultimatum: hand over the Omega keys, or they expose Jack, Miko, and Raf to Cybertron's poisoned atmosphere.
Clip Show: "Grill," parts of "Toxicity," and "Patch."
*Click* Hello: Arcee pulls one on Starscream in "Darkness Rising, Part 4" when he threatens to kill Fowler if the Autobots don't back off. Further establishing that this Starscream is awesome, even this doesn't make him back down.
She pulls it off again in "Rock Bottom". He doesn't handle it as well.
Cloning Body Parts: Starscream ultimately replaces his lost T-Cog with one salvaged from one of his dead clones.
Also done by Ratchet (whilst under the effects of synthetic Energon) in "Stronger, Faster", to a Vehicon miner. With a blowtorch.
There was also Starscream who did this to Agent Fowler to get the location of the Autobots' headquarters.
Subverted also with Airachnid who knew that it wouldn't work on Arcee, so instead, she threatened the life of Tailgate. She meant what she said.
Knock Out implied this with Silas, who was resurrected in Breakdown's body. Knock Out is very well aware of the irony, as well as showing no intention of turning off the pain receptors this time around.
Optimus: We must never lose sight of the fact that upon this Earth, we are titans. And such power must be used wisely.
The Comically Serious: Optimus. He has his moments of warmth and friendliness but is never one to joke around with the rest of the team. As a result his unflinching deadpan reaction to the humor of others makes him just as funny.
Jack: Hey, Optimus, wanna see something funny?
In "Grill", Optimus was able to make a simple greeting hilarious. He clears Agent Fowler's insistance to his doubting superior that Optimus is still alive. Optimus promptly shows up right next to the building window.
Prime: "I am fine, General Bryce. How are you?"
Ultra Magnus is the same way, with an added layer of stern disciplinarian to it. A memorable moment in "Project: Predacon" had him ask Optimus some questions about Agent Fowler's odd quips and Optimus's response was to take him aside and say "Agent Fowler can at times be oblique. I find it best to simply nod and mobilize."
Composite Character: Arcee has more in common in her general demeanor and color scheme with Chromia than the original character. Likely an attempt to avoid the "Girls Wear Pink" cliche (she does have some pink highlights), while Arcee is still the best known female Autobot.
Bulkhead combines the personality and background of Animated Bulkhead with the heavy-hitter position filled by Ironhide in G1.
Wheeljack himself takes the name and appearance of the G1 character (with some of Ironhide's traits as well), while reminding us of Animated Prowl.
Airachnid, being a female purple and black Decepticon with a spidery look, was initially thought to be an Expy of Blackarachnia (from both Transformers Animated and Beast Wars). However, her debut episode showed her to be evil and combining Animated Lockdown's loner mentality, love of hunting, trophy collection with Rampage and Tarantulas' homicidal tendencies, and only the arachnid appearance of Blackarachnia. Her color scheme is also reminiscent of G1's Insecticons.
Inverted with regards to the Magnus Hammer of Transformers Animated; it was suggested the Magnus Hammer was used to create the container for the Allspark. The forging qualities were transferred to the Forge of Solus Prime (also a hammer) while the toy-only character of Ultra Magnus has the Magnus Hammer as simply his Signature Weapon.
Although Ultra Magnus takes up the drained Forge of Solus Prime as a melee weapon.
Megatron is a mash up of several incarnations. He's got the bucket-head (and actor) of his G1 counterpart, feral, pointy design and alternate mode of his Movie incarnation, but like his Animated incarnation, royally doesn't give a damn about anything and is The Stoic (and his robot mode also has cues of the Animated Cybertronian mode).
Conservation of Ninjutsu: Played with. The Vehicons are fairly tough, it's just that they've got Mook status and our heroes are tougher. When the Autobots fight together, an army of them gets gunned down in droves, but that can be applied to Bash Brothers. A major exception to the trope is Cliffjumper's last battle; it was seven-to-one, but he brought down three, with another two caught in the energon explosion that took him down.
Likewise the first two times we see an Insecticon, they're considered nightmarishly strong and dangerous. The first one encountered on Cybertron has to be outwitted and the second one nearly beats Megatron in a 1v1 fight. A later episode has an army of them being gunned down by the regular bots with relative ease. In the latter case, there was much more room to maneuver (as opposed to the fight with Megatron, wherein both combatants were trapped in an enclosed arena), and the Autobots had full access to their ranged attacks (unlike Megatron, whose powerful fusion cannon was webbed up and inoperablenote however, he did get one shot off, point blank in the face, it only knocked the creature back and made it angrier) as well as the fact that Insecticons are apparently highly vulnerable to blasterfire while airborne.
As the series progressed, it seems that Insecticons are most dangerous in enclosed spaces because of their raw size and strength making maneuvering difficult. In open areas, smarter fighters are better able to avoid their attacks and strike back.
In "One Shall Rise, Part 1" Unicron's avatar seems to be a reasonable one-on-one match for Optimus. By the beginning of part 2, it's been revealed that they're mooks and Optimus starts trashing them by the truckload.
The prequel graphic novel tie-in to the series has Cliffjumper and Arcee investigating Decepticon activity on Cybertron, with mention that the planet is still effectively a dead world, as it was left at the end of War For Cybertron.
Cybertron's design when shown in the series, is the exact same design used to depict the planet in War For Cybertron (just recoloured a little).
Also, Megatron is using Dark Energon in the series, which he first acquired control of in War For Cybertron. Though his and Starscream's dialogue when it is first shown in the series can give the impression that this is the first time they've seen it up close, this is later Hand Waved the very next episode by Ratchet stating that Dark Energon is such a rare substance that it's virtually non-existant, making it likely what Megatron managed to obtain is the first they've seen in millions of years. Combining that with the idea that the stuff they were using in WFC was a manufactured variant that used ordinary Energon to create it (sure enough, the Decepticons seem to have stopped using it in Transformers: Fall of Cybertron, as severe Energon shortage is a major plot-point), and that seen in the series is the natural raw stuff, and Megatron and Starscream's apparent unfamiliarity with it makes a little more sense. Adding to that, Arcee even mentions that Cliffjumper's zombified remains did resemble Decepticon experiments from during the war.
The bulk of the Decepticon forces in War For Cybertron are formed by nameless Decepticon Troopers that are purple in color and have red visors. In this series, similar troops are used, only they're called Vehicons (which is itself a nod to Beast Machines).
In the story told about the legend of Unicron and Primus, Optimus notes that Primus became one with Cybertron's Core, which as shown in the flashback, is almost identical to how it appeared in War For Cybertron, and was how Optimus acquired the Matrix of Leadership in this continuity.
The history of Optimus and Megatron told in "One Shall Rise, Part 3" is a condensed version of events that happened in Transformers: Exodus and War For Cybertron.
Optimus' broken sword remains broken, as seen in the finale of the three-part "Orion Pax" season premiere.
In "Operation Bumblebee, Part 1", Megatron mentions that he was the one who damaged Bumblebee's ability to speak, which happened in Transformers: Exodus.
In "Out Of The Past", Cliffjumper mentions The Sea of Rust and being separated from his unit.
In addition, Shockwave has also been reverse-engineering space bridge technology from the ancients in the time since Cybertron went dark. He managed to do this in Fall of Cybertron as well, but his efforts were destroyed during those events and it is even noted in the episode that it has taken him all this time just to finish recreating his work and find enough Energon to power it.
Optimus' message from Earth also says that he believes the Decepticons were planning to plunder Earth for its resources. This is exactly what they were going to do to prehistoric Earth in Fall of Cybertron, but the destruction of Shockwave's Space Bridge tower (along with the loss of Earth's co-ordinates), the fact the two factions' ships fell into an unstable Space Bridge portal, as well as the series and other fiction mentioning they spent eons warring on other planets before they came to Earth, indicates that the Decepticons have been unable to rediscover Earth's location all this time, until they came across Optimus' message.
The same episode also manages to subtly indicate Shockwave's massiveArm Cannon in place of his left arm is permanently fixed into place (such as when he has to use it to hold Arcee down). Fall of Cybertron shows he once did have a proper left arm, but it was bitten off and swallowed by Grimlock in his Tyrannosaurus rex form.
In "New Recruit", Smokescreen mentions the Cybertronian Elite Guard, from where he received his training and also wears their sigil on his shoulder pads. The group has previously featured elsewhere in the Transformers Aligned Universe, the previous Autobot leader, Sentinel Zeta Prime was once a member. Smokescreen was also a guardian and friend of Alpha Trion, who was a mentor to Orion Pax/Optimus Prime and appeared as a character in Exodus (and also made a cameo appearance with the other Thirteen Original Transformers in "One Shall Rise, Part 1"). He also mentions Halogen, a member of the Autobot High Council who appeared in Exodus and approved Alpha Trion's decision to make Orion Pax the next Prime, only to be assassinated by Megatron for it. He also offhandedly refers to the Constructicons, who made appearances in Exodus and were mentioned in Fall of Cybertron.
Convenient Color Change: Putting Dark Energon into himself changed Megatron's eye color, and doing the same to his ship, the Nemesis, made it change from blue power lines and purple screens to purple power lines and red screens. Oh, and also sentient.
The latter is justified by both the Exodus/Exiles novels and War For Cybertron/Fall of Cybteron, which state that the Nemesis was once Trypticon, whose mind was apparently decimated by the events that made him what he is now. It was never explained whether the intelligence the Ship was displaying was Trypticon's mind somehow being restored and altered by the presence of Dark Energon in his body, or something else entirely.
Cool Big Sis: Arcee acts as this toward Jack, according to her official bio.
Cool Car: Bumblebee turns into what is essentially a muscled-up version of a Chevrolet Camaro (called an "Urbana 500" in-series), while the ground-based Vehicons transform into sleek black vehicles with purple tints. MECH is also outfitted with their own vehicles, seemingly with custom paint jobs.
Cliffjumper turns into an old-fashioned Dodge Challenger with bull horns on the hood.
Curb-Stomp Battle: It's been mentioned a few times on here, but it feels nice to sum it up here: Megatron or Optimus vs anyone (other than each other) equals this, not counting Airachnid's sneak attack on Optimus in "Partners". The best example is a literal version of this, with Soundwave owning Airachnid.
Curb Stomp Cushion: Sometimes characters are completely outmatched but they get a few good shots in. One example is Megatron vs. the Autobots sans Optimus in "Orion Pax: Part 3." Never before has Megatron's versus the regular soldier been more apparent, but Bumblebee and Arcee deserve a lot of points for jumping in regardless and Bulkhead and Ratchet refused to stay down for long.
Another example is Ultra Magnus and Wheeljack vs. Predaking in "Evolution." They went in for amazing Bash Brothers battle against The Juggernaut. They even briefly have a Hope Spot that they had a chance at winning, but that ended swiftly. The only consolation they got was they managed to set aside their differences and earned each others respect for how well they fared given the circumstances.
Cute Mute: The few times Bumblebee speaks, it's in digital beeps and whirls that, among the humans, only Raf can understand (and he does so immediately), whereas the other Autobots seem to have no trouble understanding him. The thing is, that's probably native Cybertronian, and his vocal processor would allow him to speak in English, and since that was destroyed, he CAN talk, just not in human tongues.
Bumblebee manages to use this to Bluff The Imposter, since Silas (as Nemesis Prime) can't understand him, either.