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The Starscream clones haven't done much, but Megatron did show why he's the Big Bad and Starscream's The Dragon. In the two-part season finale, Megatron gets hit by an explosion with a 100-mile radius in a small Deus ex Machina ball of Heroic Sacrifice. And all that does is damage him enough so that Optimus Prime can take him down with the Magnus Hammer.
On Beast Wars, The Dragon role for Megatron is a little more sketchy, as it seems Dinobot fulfilled that role before his Heel-Face Turn in the pilot episode. Later characters shifted in and out of the role, but it wasn't until Megatron put a Restraining Bolt on the psychotic Rampage that we had a solid Dragon. Dinobot II filled the role better later on because he was more loyal to Megatron.
Now that Megatron has reawakened and Starscream has deserted him it appears Airachnid and Knockout have become Co-Dragons. Though when Airachnid tries to order the Decepticons to abandon Earth (and Megatron), Soundwave steps in and effortlessly stops her power grab.
After Airachnid's failed power-play she's still working for the Decepticons, but Soundwave seems to have supplanted her as The Dragon.
Airachnid eventually goes rogue, at which point newly-introduced Dreadwing is promoted the second-in-command position.
Interestingly, when Megatron realizes that Unicron's resurrection is imminent in the season one finale, he attempts to position himself as Unicron's Dragon. Unfortunately for him, Unicron considers him beneath notice which leads the infuriated Megatron to enter an Enemy Mine with Optimus to take Unicron down.
The Fallen is usually this to Unicron, betraying the other twelve original Transformers in the process.
This character concept is parodied on Adventure Time by Gunter, the Ice King's favourite penguin.
In The Legend of Korra, Amon's second-in-command, credited as 'The Lieutenant', is by no means a slouch following orders. He's taken on the Avatar and her friends plenty of times and has proven to be very formidable; good enough to shock them into unconsciousness more than once. Actually, The Lieutenant shares this role with Hiroshi Sato.
Saikhan was briefly the dragon to Councilman Tarrlok.
Korra's uncle Unalaq is revealed to act as this to Vaatu, the ancient spirit of darkness, though between working for his own ambition, Vaatu not being able to directly accomplish anything until Unalaq frees him, and the two of them ultimately merging into one threat as the Dark Avatar, they could be considered a Big Bad Duumvirate instead. It is later revealed Unalaq used to be The Dragon to Zaheer within the Red Lotus, but betrayed Zaheer to their enemies.
Zaheer has Ghazan, who is his most loyal follower.
From Jem episodes: "The Beginning" to "Hot Time In Hawaii", Zipper is the Dragon for Eric Raymond. Zipper is arrested by the Holograms. In the same cartoon, Techrat and "The Stingers" could be considered Dragons to Eric at different times.
There are plenty of dragons in Teen Titans and a clear tendency among them to turn on their masters, beginning with Slade's failure to properly inspire Robin's loyalty or fear, continuing with Terra blasting him into a pool of lava, and Bumblebee very soon after her introduction as Brother Blood's apparent second in command. In the fourth consecutive season, Slade gets to be the dragon to Trigon. No points for guessing how that goes. In the fifth season, The Brain had much better luck with his Dragon (part of his Quirky Miniboss Squad) in the form of Monsieur Mallah: those two got their asses kicked together.
In season five, we actually see Co-Dragons. Monsieur Mallah is very often seen in the company of The Brain, but does not do much for the majority of the season except act as his personal body guard. The 'Enforcer' portion of that is sidelined to Madame Rouge, who is frequently seen as a terrifying opponent able to defeat numerous Titans with brutal efficiency, including Robin.
Kalibak isn't really Darkeid's dragon - he considers him an annoying and incompetent liability, and refuses to let him fight Superman. Desaad or Granny Goodness are probably better examples.
Mercy Graves probably counts as Lex Luthor's Dragon as a Ninja Maid type, but outside of her memorable Cat Fight with Harley Quinn in the "World's Finest" crossover, she never got to do much Dragon-ing. (After all, when your main adversary is Superman...)
The premiere of Batman Beyond has Mr. Fixx as Derek Powers' bodyguard, hit man, and all-around Dragon. He's killed off by the time it's over, but that's okay — a little dose of I Love Nuclear Power, and Mr. Powers is set for the season.
In the second series, Raythar and then Shagon serve as The Dragon to Nerissa at various points. Raythar then briefly takes over Cedric's Dragon role to Phobos, before Cedric goes all Starscream and takes over, making Miranda his Dragon. Villainous second-in-commands for everyone!
Code Lyoko features Season 2 newcomer William Dunbar as the unwilling Dragon for an immaterial Big Bad in Season 4. Ironically, while William is "resurrected" numerous times after the heroes "destroy" him, his appearances are never treated only as annoyances, but instead are considered a real threat every time, thus keeping him from entering Mook territory.
Before this, in Seasons 2 and 3, a unique monster called "Scyphozoa" was fulfilling this role, directly enabling XANA's scheme (unlike the ordinary Mecha-Mooks). After William's conversion, the Scyphozoa was never again seen at the same time in Season 4.
In the 2003 series, the role of the Shredder's dragon is initially filled by Hun, the Lightning Bruiser leader of the Purple Dragons gang. Eventually, he comes to share the role with female ninja Karai. Later on still, the role is taken by Master Khan, a Foot member trying to bring the organization back together after its apparent dissolution.
Gobots: Crasher is Cy-Kill's giggling, psychotic henchwoman and is genuinely more powerful, more threatening and above all else, scarier then he is.
Fright Knight from Danny Phantom acted as one to both Pariah Dark and Dark Danny. It seems he would have played the same for Vlad, but their alliance is left ambiguous due to the original writer leaving.
And occasionally, Skulker plays this role to Vlad.
Allan in Tintin is the closest the series has to a Dragon. First he's an associate of Omar Ben Salaad, then ultimate Big Bad Rastapopoulos. A bullying, volatile, aggressive creep, the only person he kowtows to is his boss of the time, although he doesn't always respect him. His longstanding relationship with the Captain means he's good at mental cruelty too.
Jonny Quest episode "Dragons of Ashida": Sumi to his master Dr. Ashida.
In The New Adventures of He-Man, Skeletor was demoted to Dragon for the Big Bad Flogg. However, Skeletor was constantly manipulating Flogg from behind the scenes. In the action figures' mini-comics (and the revised Masters of the Univers Classics continuity), the roles were reversed.
In X-Men: Evolution, Mystique starts out as the Dragon to Magneto, before striking out on her own in the second season. Sabretooth then seems to take over the Dragon role. Later on, Mesmero serves as the Dragon to Apocalypse.
In Buzz Lightyear of Star Command, Warp Darkmatter is the Dragon to Big Bad Zurg. Though once the TV series started, that relationship seems to have ended, as Warp had since gone freelance.
The History episode of Home Movies has a comedic example: Evil George Washington, Picasso and Annie Oakley are planning to destroy the human race and George unveils his "killing machine, who also happens to be [his] favorite kitty" Mr. Pants, who is introduced with a catchy rap song.
Mr. Pants: I'm the roughest, toughest kitty in the land/My name is Mr. Pants, I'm the kitty cat man/Nobody's gonna stop me from having my way/My name is Mr. Pants and have a nice day
In Supernews, Steve Jobs has The Finder do his bidding and track down Bill Gates when they have their nerd wars.
In the Disney version of Robin Hood, the Sheriff of Nottingham is clearly Prince John's Dragon. He's a constant physical threat, leads the squads of Mooks in their attempts to capture Robin, constantly (and relatively loyally) takes orders from his (somewhat) brighter boss, and serves as Robin's final opponent during the movie's climatic battle. Not bad for an overweightwolf with a Southernaccent.
Disney's Aladdin has Iago, Jafar's parrot, who makes trouble for our heroes in stealing their posessions, decieving them with fake voices, and acting as a sort of sentry before the final conflict.
The TV series had Haroud as Abis Mal's Dragon, despite almost every line Haroud says to him is dripping with sarcasm, he never actually becomes The Starscream. Also, Xerxes is to Mozenrath as Iago was to Jafar.
The hyenas in The Lion King work this way, especially since Scar doesn't want to reveal his role as the Big Bad.
In The Venture Bros., #21 Took a Level in Badass following #24's tragic death and became the Monarch's top mook, inspiring and training the rest of the butterfly troops to new heights of efficiency in henchmen. Two-Ton Twenty-One played a huge role in making Monarch a true menace once again.
Dr. Girlfriend was originally this, but one of her conditions for marriage was to upgrade the relationship to a Big Bad Duumvirate.
In Phineas and Ferb The Movie: Across the 2nd Dimension Alternate Dimension Doofenshmirtz captured and defeated his dimension's Perry the Platypus and turned him into Platyborg, the General of the Norm-bot army. Platyborg is the Dragon, and the Norm-bots are sort of "sub-dragons."
Wayland Smithers Jr. from The Simpsons is actually this to Charles Montgomery Burns.
In the Looney Tunes short "Knighty Knight Bugs", Yosemite Sam as the Black Knight actually has a dragon for a sidekick as part of his evil plan to prevent Bugs Bunny from retrieving the Singing Sword, but he constantly messes things up. At the end of the short, Sam and the dragon are tricked inside a castle tower full of dynamites, and he warns the dragon not to sneeze otherwise he will send them both blasting off into space. The dragon sneezes, and as a result the entire tower flies off to the moon with the two still inside.
Sam: Dragons is so stupid.
Megamind has Minion, who helps design his costume and is the only friend he has.
Since Megamind has become a superhero, Minion will now be his sidekick instead of his Dragon.
Lex Luthor: "Young man, if you expect to detain me, please contact my attorney."
Motorcity: Has three main antagonists and thus three Dragon's. Kane has Tooley, an idiotic but loyal man, Kaia has Rall, a shirtless terra with a mohawk whom she gives orders to and accompanies her into battle, and The Duke of Detroit has a red headed woman known as "No. 2" (possibly fitting the trope concept).