In season 1, Ira Gaines is The Dragon to the Drazens.
In season 2, Peter Kingsley is The Dragon to Max, Trepkos and several oilmen.
In Season 3, Hector Salazar served as Dragon for his brother Ramon. Marcus Alvers was Stephen Saunders' own Dragon.
In Season 4, Navi Araz and several others serve as Dragons to borderline Karma Houdini Habib Marwan
In season 5, Christopher Henderson is The Dragon to Charles Logan.
In season 7, Ike Dubaku is The Dragon to Benjamin Juma. Greg Seaton and Stokes were Hodges' Dragons, with Seaton serving as his right hand and advisor and Stokes as leader of the Mooks. Cara Bowden and Tony were Wilson Co-Dragons, though Tony was actually a Dragon with an Agenda
In Season 8, a Dragon Roost Lugo Elson was Vladimir Laitanan's Dragon. Tarin Faroush was the Dragon for Samir, who in turn was also The Dragon for Farhad Hassan and a number of Kamistani Generals, though he turned on Farhad. Jason Pillar was Logan's Dragon, until he outlived his usefulness and became and liability. Pavel Tokarev was Dragon for Minister Mikhail Novakovich who in turn was the Dragon for President Suvarov.
666 Park Avenue: Tony seems to act as Gavin's muscle on occasion. Though now it seems he's going to hire Kandinsky to do his dirty work for him.
In Buffy's spin-off series, in Season 2 The Groosalugg served as the Dragon for the Covenant of Trombli.
In Season 3 the incorporeal demon Sahjhan tried to use Holtz as his Dragon, but he turned out to be a Dragon with an Agenda different enough that it led to him accomplishing the exact opposite of what Sahjhan wanted him to do.
The Beast was the Dragon for Jasmine before she was born. However, because his and her ultimate motives massively diverged (wanton destruction vs. Utopia Justifies the Means) she arranged for him to be killed by Angelus, who refused to cooperate with her. She had Connor serving this role until she was born, when Angel briefly took it up before Connor resumed the position.
The Circle of the Black Thorn is also the dragon to the Senior Partners, sharing this role with Hamilton (though the Circle has more power, since Hamilton is just the liaison). Well, they probably have more influence on this plain of existence, but in terms of personal power they all die easily enough (Save Cyrus Vail). Hamilton by comparison is the most physically formidable threat in the show, barring possibly the Beast or Jasmine.
Battlestar Galactica (Reimagined): The Centurions (hard-to-kill robots with miniguns in their arms) are collectively the Dragons to the humanoid Cylons who, despite possessing superior strength to humans, are otherwise relatively easy to kill.
Being Human: In series two, Professor Jaggat is introduced secretly as the scientific mastermind behind the purging of the werewolves, with Kemp as her public face - her dragon. However, towards the end, we find out Jaggat is just the one Kemp goes to when he needs to find a method of killing a werewolf or vampire, and she is in fact the dragon to him, and is dragging her feet and is on the verge of turning heel face. Occasionally, she screams stars, too Quite a mixed bag of nuts.
Buffy the Vampire Slayer: Most of the examples that seem likely Dragons end up generally being rather weaker than The Big Bad, putting them more into the category of Mini-Boss, but removing the section here would just have someone recreate it anyway. Here's the potential list anyway:
In Season 1, The Master was trapped in a church, forcing him to use other vampires for his tasks. Luke was initially The Dragon for the Master, though he didn't last very long. After that Darla took up the role, before she died too. He ended up with The Anointed One, whose draconic potential was rather limited by being physically a child.
In Season 2, the vampire preacher Absalom could be considered the A.O.'s Dragon and then it looked as if Spike was going to be The Dragon for the Anointed... but instead, as it turned out, Drusilla was The Dragon for Angelus with Spike as The Starscream.
In Season 3, Mr. Trick begrudgingly serves as a Dragon-in-Chief to Kakistos before getting fed up and leaving him to the Slayers. After this, Mr. Trick went solo, and then he and later Faith was The Dragon for the Mayor.
In Season 4 Adam, who was intended to be Professor Walsh's Dragon murders her upon awakening. In the final episode, he gains Forrest Gates as his own Dragon.
Community: Chang to the Dean in the episode Modern Warfare. He even has his own El Tigre tiger striped paintball gun. And dual gold handguns. And room-painting suicide bomb.
Deadwood: This show had two. Evil millionaire prospector George Hearst is always accompanied by Captain Turner, an old mountain of a man who serves as his bodyguard and enforcer. He apparently has a long history of killing Hearst's enemies in public streetfights. On the other side, small-time kingpin Al Swearengen has Dan Dority as his strong right hand. Al is an able combatant himself, but will generally send Dan to do the wetwork. In one notable episode, the two rival Dragons fight a duel as their masters watch from the balconies.
Doctor Who: In the series four finale, the Supreme Dalek appears to be the Dragon to Davros. However, it is arguable that Davros is himself the Dragon of the insane Dalek Caan. Similarly, Davros' questionable status in this episode could make him a Dragon for the Supreme Dalek itself.
An interesting twist is in "The Pandorica Opens" which speaks of a unstoppable being that causes death and destruction for countless races. It turns out, that being is actually The Doctor, from the point of view of the countless villains he's fought over the centuries. So from the Villains' perspectives, The Doctors' Companions are in fact HIS Dragons
Firefly: Crow was The Dragon to major villain Adelai Niska, before Mal kicked him through one of Serenity's engine.
Glee: As of halfway through Season Two, Quinn and Santana have both been replaced as Sue Sylvester's Dragons by Becky Jackson, a short, Badass Adorable Cheerio with a mean line in admin and ruthless glares. And Down's Syndrome. Nobody at Mc Kinley High is fool enough to think this means she's a Morality Pet rather than a Dragon.
Happy Days: In one episode, a gangster tries to take over Arnold's. He has a henchman with a metal claw for an arm called "The Claw" that Fonzie fights.
Season 1: Career criminal Johnny Crowder and sex offender Hestler Jones were Co-Dragons to Johnny's uncle, Harlan County gang boss Bo Crowder.
Season 2: Corrupt chief of police Doyle Bennett plays this role to his mother, marijuana kingpin Mags, in Season 2, enforcing her rule over Bennett township. Boyd Crowder hires Neo-Nazi henchman Derek "Devil" Lennox to act as his Dragon.
Season 3: Dixie Mafia bagman Wynn Duffy is hired to act as The Dragon to Detroit mobster Robert Quarles, helping him deal with the local criminals—though in a twist, Quarles is far more physically dangerous than Duffy (himself a bloodthirsty psycho).
Season 4: Boyd gets a new Dragon in the form of ex-soldier, Colton Rhodes, who is a major character for the rest of the season. We meet Detroit gangster Nicky Augustine, who acts as Mouth of Sauron to Theo Tonin, and has his own Dragon in Mr. Picker.
Season 5: With Devil and Colt both gone, Jimmy and Carl step up as Boyd's Co-Dragons. We meet Theo Tonin's most trusted killer, Elias Marcos. We are introduced to Daryl Crowe Jr., who has his psychopathic younger brother Danny as his Dragon.
Kings: Had Thomasina as The Dragon to King Silas, and damned if she wasn't an efficient one.
Part of what made Power Rangers in Space so popular was the inclusion of the morally ambiguous Ecliptor. It also had some twists concerning the enemies, Astronema was the Big Bad in the general sense, while she was more or less The Dragon for the rarely seen Dark Spector.
The Graysons have Frank until "Amanda"/the real Emily Thorne kills him.
Revolution: Captain (later Major) Tom Neville. While not Monroe's actual second in command, he appears to be part of Monroe's inner circle, and is the most recognizable villain after the General himself.
Sons of Anarchy: Season 2 had AJ Weston (Henry Rollins) fill this role for Ethan Zobelle (Adam Arkin).
Star Trek: Voyager: Seska straddled the line between this and Big Bad. She acted in Culluh's employ, doing a great deal of his dirty work, but also consistently showed herself to be a far more cunning and dangerous planner, perhaps making her the Dragon-in-Chief.
Every Goa'uld in Stargate SG-1 has a First Prime, who is his most trusted servant. A number of First Primes are aware that their masters are not gods, but they know they cannot change the way of things, so they merely attempt to "temper [their] sword". Both Teal'c and Bra'tac used to be Apophis's First Primes (Bra'tac before Teal'c). Teal'c father was the First Prime of Cronus, before he lost an unwinnable battle and was painfully executed by Cronus. Another notable First Prime is Oshu (a clone of Sun Tzu), who faithfully serves his master Lord Yu and covers for his developing mental illness.
Supernatural: Meg is the Dragon for her father Azazel in Season 1. She later serves this role to Lucifer in season 5.
Crowley is implied to have been this to Lilith off-screen.
Zachariah to Michael.
Edgar to Dick Roman.
Tessa to Death, though this is a rare good example.
Super Sentai: The parent series of Power Rangers' parent series generally had one a season. They come in all shapes and sizes, but certain commonalities exist. They tend to be swordsmen, and to have a grudge against one specific Ranger, usually Red. Said Ranger usually destroys The Dragon in single combat during the finale.
Dai Sentai Goggle Five had General Deathgiller, who was essentially this trope personified. Notably, however, he was actually ranked lower than the Evil Genius, Deathmark.
Kagaku Sentai Dynaman had Prince Megiddo, son of the Big Bad, who was eventually kicked out for being useless and replaced with Dark Action Girl General Zenobia. After he come back as the Dark Knight and killed Zenobia(indirectly) and Aton, Chimera filled this role in the finale.
Choudenshi Bioman had a very well-stratified villain hierarchy including a Dragon, Mason.
Dengeki Sentai Changeman had General Guiluke, who actually supervised most of the day-to-day villainy. Later, Guiluke is forced to step down and he is replaced with Queen Ahames. But later regained his position after he become Super Guiluke.
Chikyuu Sentai Fiveman first had Captain Galois, though he also has shades of goofiness time by time. Once he failed too many times, Chevalier gets promoted into The Dragon. And later, Galois regained the position, making the Zone to have TWO Dragons near the end of the series.
Choujin Sentai Jetman is kind of unique that there's no such thing as who gets the higher position (they're all competing for the Big Bad position). The closest you may get is probably Radiguet, who was the second most powerful one after their missing Empress Juza. He's also The Starscream through and through (against Juza and later Tranza), thus eventually elevating his position from The Dragon to Big Bad.
Chouriki Sentai Ohranger features another father-son Big Bad-Dragon relationship with Prince Buldont, who's short and dumpy at first, but gains a much more Dragony body later on. By the time he gets his upgrade his father is gone and he is the new Big Bad. Buldont's Dragon consists of a brainwashed Bomber the Great for two episodes and then his wife Multiwa, although Buldont's a hands on kind of guy so he might also technically be his own Dragon.
Gekisou Sentai Carranger has two. While Zelmodor seems to fulfill this role at first, he later gets co-opted by Ritchhiker.
Bakuryuu Sentai Abaranger has an odd example in Lije, a small girl who doesn't really fight. She's really only the Dragon by default due to all the other roles being filled. This is played more straight after her transformation in to Lijewel.
Mahou Sentai Magiranger has Victory General Branken, who's actually the boss when the show begins. He is replaced by Dark Magic Priest Meemy following his defeat, and when Meemy falls, the Infershia Pantheon steps in, led by Dagon.
Tokumei Sentai Go Busters: Enter, except here he's the Big Bad's only sapient underling. Later after the first defeat of Messiah, Escape(unwillingly) fall into this position for Enter.
Zyuden Sentai Kyoryuger: While Many Faced High Priest Chaos is the second in command, his boss was unable to come and do anything until the finale, making Chaos the Big Bad and putting Raging Knight Dogold as The Dragon. Later, however, Knight of Hatred Endolf was created, and he started competing with Dogold for Dragon status. After it seemed Dogold won by possessing Endolf, it's revealed that Endolf was biding his time to get his revenge and make Dogold his own Dragon. In the end, Dogold teamed up with the Sixth Ranger to take down Endolf before allowing himself to die, but by this point, the actual Big Bad was revived and Chaos had become The Dragon.
The Thick of It: While his boss was more of an Anti Hero than a full on villain, Jamie McDonald functions as a rather competent Dragon for main character Malcolm Tucker. That said, he did have some ambitions of his own, which may account for his absence in the third series.
The Wire: Stringer Bell fills this role for Avon Barksdale during the first half of the series, and Chris Partlow fills it for Marlo Stanfield during the second half.
This seems to be the role of Slim Charles, no matter who he works for. He starts out working for Avon, and moves up to the point where he almost supplants Stringer, then works as #2 for Prop Joe. He tells Marlo that he "ain't cut out to be no CEO" when Marlo tries to give him half of Joe's old territory, and is seen alongside another drug lord in the finale montage.