Yggdrasil has Craniamon/Craniummon, Gallantmon/Dukemon and Omnimon/Omegamon as Co-Dragons.
Captain Ginyu is Frieza's Dragon in Dragon Ball Z. He's even Genre Savvy enough to know that he's the Dragon when he correctly assumes that Goku's ultimate goal is to take on Frieza, though apparently he's not savvy enough to predict his own inevitable defeat.
The Vision of Escaflowne has Dilandau as Folken's Dragon, who in turn is Dornkirk's Dragon. (While Folken doesn't fight, he is the tactician, and fills a very Vader-esque role)
Fullmetal Alchemist has Pride, the oldest and most indispensable of Father's homunculi. An Enfante Terrible with a sadistic streak and a Lack of Empathy that's truly staggering, Pride's ability to utilize shadows as weapons makes him all but indestructible, and he seems to take the heroes' interference in Father's affairs very personally. Despite that, he's loyal to Father to the point of mortally injuring himself to ensure that the latter's plan to become God will succeed.
Great Mazinger: The Great General of Darkness was the first Dragon of The Emperor of Darkness. After his death he was replaced with the Grand Marshall of Hell who is none other than a resurrected Dr. Hell now as a gigantic cyborg.
UFO Robo Grendizer: Great King Vega had several Dragons throughout the series, but the main ones were Commander Blackie for as long as he was alive, General/Lady Gandal and Science Minister Zuril.
In every Sailor Moon season except the last one, the first villain whom the audience believed to be the Big Bad was not, and was paving the way for an even more powerful Big Bad.
Season 1: Queen Beryl to Queen Metalia.
Season 2: Prince Demand to Wiseman/Death Phantom.
Season 3: Mistress 9 to Pharao 90.
Season 4: Zirconia to Queen Nehellenia.
Season 5: Galaxia to Chaos.
Yu-Gi-Oh! and its various spin-offs have Rafael, Rishid/Odion, Manjoume, and Trueman acting as Dragons to Dartz, Marik, Saiou and Darkness respectively.
In Yu-Gi-Oh! 5Ds, it could be argued that Rudger/Roman Goodwin was his younger brother Rex's Dragon. Also, the Three Emperors of Yliaster, a.k.a. the Infinity Trio, whilst first appearing to be the Big Bads of season two, are Dragons to ZONE. Actually, make that "Dragon" since they've combined into their true form, Aporia.
Noah Kaiba, who appears to be The Big Bad of the Virtual World filler arc is actually The Dragon to his father, Gozaburo. Within Noah's Quirky Miniboss Squad, The Big Five, Lector is The Dragon to Big Bad Ganzley. He holds all The Big Five's best cards, and unlike most of them, has the makings of a solid competitive duelist. During their 5 on 2 duel against Yugi and Joey, his takeover of The Big Five's strategy is foreshadowed heavily and played as a very bad thing.
Akhenaden, becomes this to Zorc after Zorc is revived. Present day he is a Big Bad Duumvirate with Dark Bakura.
Legato Bluesummers to Knives Millions in Trigun. Oddly, his physical strength is in fact below average, and his primary strength is his mind-control ability.
NORA: The Last Chronicle of Devildom uses Fall as the Big Bad with Deuce serving as The Dragon
In Monster Rancher, the evil overlord Moo had General Durahan as his Dragon.
Debonair/Kiishim in Tsubasa Reservoir Chronicle serves as The Dragon during one of the first missions though in a triple subversion of the trope, she is both smarter than her boss, is being made to serve him via mind control, and is in the end the one who gives him what's coming to him.
In a slightly more series-wide capacity, Kyle Rondart, who you actually meet very early in the series, turns out to be The Dragon for Fei Wang Reed, the series' Big Bad.
Chloe in Noir can be seen as The Dragon to her mother figure/boss Altena, and whether this was in fact part of Altena's plan is hotly debated among fans.
The Big Bad of Code Geass, Charles zi Brittania, has Sir Bismark Waldstein, the Knight of One. And in episode 21 of R2, Suzaku (Meaningful Name as Suzaku means "Vermillion Phoenix" The Four Gods! One wonders why they didn't give him the name Seiryuu instead!) has become Emperor Lelouch's Knight of Zero aka his Dragon and thus likely to be remembered for ending up as this, since he also faked his death whilst acting as Emperor Lelouch's second-in-command.
Signum from A's hits most of the benchmarks for a common variant: Leader of the Big Bad's personal forces, check. Stoic swordswoman demonstrating as much honor as her duties permit, check. Considerably more fearsome close-quarters combatant than the Big Bad, check. Personally commanding the hunt for the energies needed to grant her master Ultimate Power via an Artifact of Doom, check. Doing so in secret from her master (who in fact explicitly ordered her not to do this) in a desperate effort to save said cripplednine year oldorphan'slife, che- wait, what?
Quattro is quite possibly the best example of The Dragon in StrikerS. While Uno is technically Jail's "second brain", Quattro has a lot more screen-time, is loyal to Jail Scaglietti until the end and also has the most notable defeat of all the Numbers. Well, it can be said that Quattro, Uno and Tre (the strongest Number) are Co-Dragons to Scaglietti.
Maki Ichinose is Jin Kariya's Dragon in the Bount arc.
In the Shusuke Amagai arc, Hanza Nukui serves as Kumoi's Dragon, until he falls in battle against Ichigo and is replaced by Makoto Kifune.
Gin Ichimaru and Tousen Kaname serve as Co-Dragons to Aizen. There's also a subversion as Ulquiorra is set up to be Aizen's Espada Dragon. However, when Ichigo finally calls him out on it, Ulquiorra reveals that he's only the fourth Espada and therefore Ichigo (and the reader) is mistaken to believe there are any Espada Dragons at all.
Subverted in the Lost Agent arc: Shishigawara appears to be Tsukishima's dragon. In fact Tsukishima himself is the dragon, to Ginjou.
In the The Thousand-Year Blood War Arc, Haschwalth is The Dragon to Yhwach, The Emperor of the Vandenreich. Until Yhwach makes the Genre Savvy decision to replace Haschwalth with Uryuu Ishida. Yhwach seems to know a protagonist only joins the villains to betray them from within, so he makes sure Uryuu is immediately Kicked Upstairs to Dragon and Unexpected Successor, angering the army (which is primarily loyal to Haschwalth) and depriving him of the freedom or support to attempt a coup.
Kinnikuman has several official Dragons and several de-facto ones. The Throne arc upped the ante by having the six teams having their own Dragons in the form of second-in-commands.
Kinnikuman Team: Initially Terryman, then Robin Mask took his place
Flight Team: King 100 Ton
Strength Team: Cannonballer
Technique Team: Parthenon
Brutality Team: Buffaloman
Intelligence Team: Mammothman, demoted by the Omegaman during the finals.
Younger Toguro is Tarukane's Dragon in the Yukina arc of YuYu Hakusho. To some degree, he is a Dragon for Sakyo, but while Sakyo's plan threatens the world, Yusuke and his team are more concerned with Toguro.
We later find out that Pain, the apparent leader of Akatsuki, is actually the Dragon to "Madara Uchiha"/Tobi, the series Big Bad. To go further down the rabbit hole, Tobi himself is simply carrying out the Evil Plan of the real Madara.
Black Zetsu to Kaguya
Nosferatu Zodd of Berserk becomes Griffith's Dragon some time after the Eclipse.
Another great example is Grunbeld, who actually turns into a giant dragon in his full Apostle form.
During the Golden Age arc, Guts himself can count as Griffith's Dragon, especially if you consider Griffith's overall goal.
Sidematerials reveal that Gihren's secretary, Cecilia Irene, was this to him in a political sense, acting as his confidante, Number Two, and liason to the general staff, while simulataneously arranging assassinations and other dirty jobs.
Interestingly, you can almost always tell who the dragon is because he will usually fight Zoro, while the big bad fights Luffy
Starjun acts as the Dragon of Midora (the boss of the Bishokukai and the Big Bad of the series) and a primary fighter of the Bishokukai as well as the organization's second strongest member after the boss himself.
There are plenty of cases in Gash Bell. For starters, you could consider that every single demon is a human's Dragon, or vice versa, depending on who has the brains of the operation. Other than that, there's a classic example in the huge, hulking monstrosity known as Demoruto/Demolt as Zophise's/Zofis's Dragon. Brago even states at one point, "If it's just about power, the power I sense over there is greater than Zophise's."
One could also say that Faudo is Riou's Dragon, what with him planning to use its power to win the fight for the Demon King while hiding safe and sound inside his brain. However, going off of Mamodo, the best fit would be Zaruchim; out of all the Faudo cultists, he was the only one who was loyal to Riou. Everyone else joined either because they wanted to usurp Faudo's power or because Riou blackmailed them by cursing their partners.
Also, Clear Note, the biggest Big Bad of the series, has Goomu as his Dragon.
In S Cryed, Ryuuhou is the Dragon to Martin Jigmarl. Slight subversion in that Jigmarl is actually much stronger than Ryuuhou, but using his alter power would cause him to age insanely fast and kill him after one battle.
...At least, that's how it starts out. In the endgame, it turns out to be A Brainwashed and Crazy Biff (the very first opponent Kazuma faced) and Jigmarl himself acting as * snrk* Double Dragons to the show's trueBig Bad, Kyouji Mutou.
The real kicker? Ryuuhou winds up being the one to defeat Jigmarl.
In Part 4, Yohikage Kira's own father, Yoshihiro Kira, is his Dragon.
Part 5 has a subversion. Doppio Vinegar appears to be the most trusted subordinate of Diavolo, to the point that Diavolo has entrusted him with the power to use his stand, King Crimson. In reality, Doppio is Diavolo's split personality. The two are actually one in the same.
Mr. Heart serves the role of Shin's Dragon in the Fist of the North Star manga. In the anime, this role is filled by Filler Villain Joker after Heart is killed early in the Southern Cross arc. The closest thing Raoh has to a Dragon in the original manga and anime series is Ryuga of Sirius (in The Movie, this role is perfectly filled by Uighur the Warden).
In the Legends of the Dark King spinoff, Souga was Raoh's main right-hand man until his position is usurped by Ryuga's arrival.
Fang of the Sun Dougram gives the Designated Villain Donan Cassim not one, but two Dragons - one for the war effort against the heroes and their La Résistance friends, and the other for his political maneuvers back on Earth. Surprisingly, his political Dragon is colonel von Stein - the highest ranking officer in Cassim's army, while his military Dragon is actually his secretary Le Coque, who later usurps his role as the Big Bad.
In Umineko no Naku Koro Ni we have Kinzo as The Dragon in multiple games, and in the showdown in EP 4, Kinzo actually becomes a dragon.
In Death Note, Light Yagami ultimately acquires one in the form of Teru Mikami (who even gets nicknamed the Hand of Kira).
Tatsumi from the horror manga Shiki is the one to convert the citizens of Sotoba to vampirism when his superiors, the Kirishiki family, just hang around in their mansion.
Tomo from Fushigi Yuugi: we don't see as much of him in the anime, but in the manga he's the closest thing Nakago has to a confidant as well as a lieutenant, and his ability to kill large groups of opponents without them realizing he's even present makes him quite dangerous.
The anime adaptation of Magic Knight Rayearth adds Inouva to the cast of villains. He has the title of "Vice Commander" and often gives instruction or admonishment to the other minions in place of Zagato.