The Lensman series is built on Dragons behind Dragons. Along about the end of each book ... or the beginning of the next ... it's revealed that the Big Bad just defeated was The Dragon for someone even higher up. The stories were rewritten after their original appearance so that the reader is let in on who the real Big Bad is at the beginning of Book One, but the protagonists don't find out until Book Six.
The Mouth of Sauron may be considered a co-dragon. However, he doesn't present any real challenge — physical or intellectual — to the heroes in either the book or the movie adaptation; and appears to function strictly as a communication tool.
In Unfinished Tales it's also mentioned that Sauron (still the Necromancer of Dol Guldur at that time) intended to co-opt Smaug (the dragon from The Hobbit) as a Dragon both literal and an example of this trope - but was thwarted when, ultimately thanks to actions by Gandalf, Smaug was killed during the events of that book.
In the Film at least, Gothmog played this role to the Witch-King himself during the Battle of Minas Tirith.
Walter o'Dim in Stephen King's The Dark Tower series serves the enigmatic Crimson King. He's a Dragon-in-Chief considering that the Crimson King is just a frail, crazy old man... albeit one with a lot of bombs at his disposal.
Lord Voldemort has a number of these and juggles them.
Lucius Malfoy was originally Voldemort's Dragon. He hands missions like the one at the ministry in book 5 to the cool-headed Malfoy. Then after losing the prophecy in The Order of the Phoenix the Dark Lord decided he'd failed one too many times. Lucius spends most of The Deathly Hallows doing little more than sitting in his chair at Death Eater meetings and quietly whimperingnote it really doesn't help that Voldemort "borrows" his wand and promptly loses it. Then he and his family make a Heel-Face Turn ...
Bellatrix Lestrange — the ruthless and devoted lieutenant but isn't one of the world's greatest thinkers, so
Snape knows too much about Hogwarts and the Order of the Phoenix to be wasted somewhere else, and since he's Voldemort Double Agent inside the Order of the Phoenix he reports directly to him and no one else. He's also Dumbledore's Double Agent, which is another reason for Voldemort to keep an eye on him.
When Umbridge took over Hogwarts, Filch served as her Dragon. Additionally, Umbridge herself seemed to be Cornelius Fudge's Dragon, although she would easily qualify as a Dragon-in-Chief since Fudge was more of a Horrible Judge of Character than a villain. After the Death Eater takeover of the Ministry, she serves as Yaxley's Dragon.
The Chamber of Secrets has a literal example. The basilisk is the Dragon and Tom Riddle is the Big Bad. It's even the classic scenario: to save the Damsel in Distress, The Hero battles the Dragon and then defeats the physically weaker Big Bad. He also marries the damsel, though not until many years later.
Basta, the knife-wielding henchman to Capricorn, who runs all his errands and does most of his dirty work.
The Adderhead's Dragon The Piper.
Discworld: If Lord Vetinari was an the Evil Overlord, then Samuel Vimes would be his Dragon. Vimes is often said to be Vetinari's "terrier", often unwittingly or unwillingly, but is The Protagonist of all the Watch books.
In The Crystal Shard, Errtu was Akar Kessel's Dragon, especially since most of Akar's power is derived from the Crystal Shard, while Errtu is a powerful demon in his own right. In the rest of Drizzt's adventures, Artemis Entreri is often The Dragon.
In The Dresden Files, every villain has at least one Dragon that Harry has to deal with before he can tackle the book's real villain.
Deirdre is The Dragon to Nicodemus, her father and lover.
Tessa, Nicodemus' actual wife, uses both Rosanna and Magog as her Dragons.
Also, Lara Raith serves as Dragon and Bastard Understudy to her father (who used rape to establish control of all of his daughters except the youngest) until the events of Blood Rites, after which she is in charge of the White Court through control of her father.
In Dead Beat, the Corpsetaker uses a ghoul named Li Xian as her enforcer, though he mostly just hits things while she holds them in place with her mental powers.
Aurora had a Sidhe Lord, the Winter Knight Lloyd Slate, and a Centaur as her dragons.
The Faerie Queens all use a mortal agent known as a Knight to serve as their assassins and enforcers in the mortal world, as they cannot directly act against mortals.
In Changes, the Red King uses a pair of assassins known as the "Eebs" and a massive, difficult-to-pronounce beast that Harry dubs the "Ick" as his Dragons.
The Skinwalker serves as the Black Council's Dragon in Turn Coat, and Binder is Madeline Raith's Dragon as well.
In Ghost Story, Evil Bob plays this role for the Corpsetaker.
The Forsaken are the Dark One's most powerful mortal servants, and the most powerful of them is Ishamael, who is the Dark One's right hand. After he dies, the rest compete viciously for the vacated position of Nae'blis, which basically means The Dragon. The position ultimately goes to Moridin, an apparent newcomer who is soon revealed to be Ishamael in a new body. Subverted by Shaidar Haran, who initially appears to be another Dragon but is actually a sort of extension of the Dark One's own will, and is discarded once the Dark One's prison weakens enough that he's no longer needed.
This is played interestingly during the Last Battle across several levels. The Dark One is the Big Bad. Moridin is his Dragon, but he's not the type to get physical or lead his own troops into battle. Therefore his Dragon is Demandred, the Shadow's greatest general, who is also a Dragon with an Agenda, since he only cares about defeating Rand, not advancing the Shadow's cause. His Dragon is Mazrim Taim who acts as his enforcer in the ranks and leader of his Dreadlords, and who also schemes to take over from him.
Among the Children of the Light, the tough, skilled blademaster Eamon Valda is blackmailed into serving as a sort-of Dragon to the elderly, frail Rhadam Asunawa.
Ironically, Lewis Therin Telamon is called "The Dragon" but is not an example of The Dragon trope, but The Chosen One, as is his Reincarnation Rand al'Thor, "The Dragon Reborn".
In A Song of Ice and Fire, the physically indomitable Gregor Clegane serves as a Dragon for House Lannister, frequently being given the most dangerous, brutal and intimidating missions possible.
Gregor's closer to being The Brute though, isn't he? If Tywin has a Dragon it's Jaime (who due to his early capture doesn't see much action in the early parts of the series). In other examples, the mercenary Bronn serves as Tyrion's Dragon, and Sandor Clegane is Joffrey's.
A Song of Ice and Fire is full of Dragons, since there are almost as many factions as characters and the better part of them are either overtly nasty or neutrally antagonistic. Euron Greyjoy has Victarion (for now), Roose Bolton has Ramsay, Hizdar zo Loraq has Khrazz, The Tattered Prince has Caggo, Selys has Axell Florent, and so on, and so on.
In the physical world, the Malazan Empress has her Adjunct, who serves as her Number Two. And then there's the various minor gods and their Mortal Swords.
Katla is Tengil's (also literal) dragon in The Brothers Lionheart. She is as evil as Tengil and is his greatest weapon, and the only reason she is under his command is that she obeys whomever is in possession of the horn she is afraid of.
Another Sanderson example — at the end of Way of Kings, Szeth unwillingly becomes this to Taravangian when he discovers that he is in possession of his Oath Stone.
In the New Jedi Order series, Warmaster Tsavong Lah, leader of the Yuuzhan Vong warrior caste, is The Dragon to Supreme Overlord Shimrra who is in turn a puppet for Onimi, but the Warmaster doesn't know that. Interestingly, he also takes on many aspects of the Big Bad in the early part of the series, since he has free rein with the invasion until Shimrra finally takes personal command.
In Romance of the Three Kingdoms, Lu Bu is The Dragon of the early story, as his allegiance clears the way for Dong Zhuo's rise to hegemony. However, he demonstrates a capacity for being manipulated that leads to Dong Zhuo's downfall and eventually his own.
For all of the books that feature him, Kirtain Loor is The Dragon. He's allowed autonomy but ultimately cringes before his superiors, both of whom are worse than he is. Ysanne Isard recruited him and put him in charge of the underground Imperial movement on Coruscant after it fell to the New Republic. He had his own plots going, but the head of the People's Militia, nominally there to stop Loor, recruited him to further his own agenda. Interestingly, neither he nor his superiors ever engaged in direct or even starfighter combat with the New Republic; Loor mostly sent stormtroopers and operatives after them, and later started setting bombs and directing speeders filled with explosives into population centers. He didn't even see any New Republic protagonists until he tried to surrender some information in exchange for his life.
Dah'mir of The Dragon BelowEberron trilogy is The Dragon to the Master of Silence, a daelkyr. And an actual dragon...
In Andy Hoare's White Scars novel Hunt for Voldorius, Nullus to Voldorius.
In the eBook Legend of a Hero: Ice and Wind, ironically, the Big Bad IS a Dragon (7,000 years old and counting...) called the Dragon of the Ice, or the Ice Dragon. Its Dragon is a fire-wielding general named Marko Terror...HIS Dragons (if he were the Big Bad) would be (besides the multiple Captains) Alba T. Ross and Maria Terror, his niece.
In Paul Kelly's 'The Lost Brigade', General Arras Kierhenan is most certainly the Dragon to Eustace 'The Evil' De Mharburg's Big Bad. Unquestioning and subservient, Kierhenan is always ready to fulfil De Mharburg's orders, no matter what they may be...
In Charlie Bone, Ezekiel Bloor had Manfred Bloor, Dr Bloor, Yolanda and Yorath Yewbeam, Count Harken Badlock, Lord Grimwald, Titania Tilpin and Ashkelan all as Dragons at different points in the series.
Redtooth and later Darkclaw to Cluny the Scourge in Redwall.
Cluny goes through a long series of Dragons, since none of them lasts very long. After Darkclaw dies Cluny favors Scragg. After Scragg dies, he sets up Cheesethief as a Dragon just so he can serve as a decoy and get killed. By the final battle, Killconey loosely fills the role, and after that it ceases to matter.
Brogg (temporarily replaced by Cludd) and Ashleg to Tsarmina Greeneyes in Mossflower.
In Mariel of Redwall, Greypatch was this to Gabool the Wild originally. After his desertion, seven dragons were sent to retrieve him: Garrtail, Orgeye, Flogga, Catseyes, Riptung, Hookfin and Grimtooth.
Klitch and Deathbrush to Feragho the Assassin in Salamandastron.
Gurrad was Badrang's assassin briefly in Martin the Warrior.
Nightshade to Swartt Sixclaw in Outcast of Redwall.
Lask Frildur, Sagitar Sawfang and Grall to Ublaz Mad Eyes in Pearls of Lutra.
Ripfang, Doomeye, Karangool, Grand Fragorl and Groddil to Ungatt Trunn in Lord Brocktree.
Riftun to Kurda in Triss.
Glimbo to Raga Bol in Loamhedge.
Shard to Gulo in Rakkety Tam.
Atunra to Riggu Felis in High Rhulain.
Magger to Vizka Longtooth in Eulalia!.
Veeku and Sicariss to Korvus Skurr in Doomwyte.
Zwilt the Shade and Dirva to Vilaya in The Sable Quean.
Shekra, Mowlag and Jiboree to Razzid Wearat in The Rogue Crew.
There are many in Warrior Cats due to almost all the villains being connected in some way.
Blackfoot serves as Brokenstar's dragon in the first half of the first arc and Tigerstar's dragon in the second half of said arc before his Heel-Face Turn at the end.
Early on in the first arc, Darkstripe serves as Tigerstar's dragon until Tigerstar finds a better one.
Bone is the dragon to Scourge in the sixth book, The Darkest Hour.
In The New Prophecy arc, Hawkfrost serves as Tigerstar's dragon. He's also a Dragon-in-Chief, seeing as Tigerstar is dead but he isn't. However, he spends the Power of Three arc as a regular dragon due to Brambleclaw killing him.
The Ice Cream Psycho in Lovely Assistant (by Geoph Essex) serves as The Dragon for the bad guys. Although in the climax, there are hints that he may have been The Man Behind the Man (or at least a Dragon with an Agenda) in the first place.
Big bad Caine Soren has sadist and on-off best friend Drake Merwin...Before throwing him down a mine shaft at the end of book 2.
As of book 3 and onwards, Penny the monster bringer reprises Drake's role.
Although, Argubly, Drake is still the dragon, only now to the "thing in the mineshaft".
Firebird: Tel Tellai is Phoena Angelo's right-hand-man. He oversees security and the day-to-day operation of their resistance group when she is busy with other matters, and personally supports her as a friend and, later, husband.
Fusion Fire: Dru Polar is the Shuhr's strongest telepath, the head of Testing, and Brennen Caldwell's direct captor. He ran the attempts to extract the classified information from Brennen and he is the one who planned to break Brennen by forcing him to kill his own wife. Polar answers only to Eshdeth Shirak, who is the leader of the Shuhr.
Crown of Fire: Micahel Shirak is the son of the new leader of the Shuhr and the de facto second-in-command. He helps his father carry out their various plans and orchestrates the attempts on Firebird Angelo Caldwell's life.
Wind and Shadow: This book does not have a Dragon; instead, it has a major Big Bad and a lesser one.
Daystar: Colonel Zeimsky is Piper Gambrel's crony, creating the means to destroy the Sentinel's telepathic abilities and working to apply that "cure" to all the Sentinels. He is the scientist to Gambrel's religious bent and enables Gambrel's plans against the Sentinels to move forward. Zeimsky and Gambrel have a somewhat unusual relationship as Big Bad and Dragon, as they are frequently in conflict with each other and Zeimsky resents his subordinate role, feeling that he should be Gambrel's equal.
In Lirael and Abhorsen, Hedge manages to subvert his rival Chlorr of the Mask using Free Magic into being his Dragon, though she's got something of an Enigmatic Minion type flavor about her as well. The end of Lirael then reveals Hedge himself to not be the Big Bad as he first appeared, but The Dragon himself to Orannis the Destroyer, a tremendously powerful Sealed Evil in a Can that uses Hedge as Its agent in the outside world.
Arielle Kliest is this to the old Man in Those That Wake's sequel, What We Become.