In Sonic the Comic, Robotnik is Demoted to Dragon twice. First in the Drakon arc, he makes a deal with Emperor Ko-Dorr — the Drakons would provide Robotnik with resources and transport, and he in turn would deliver the Chaos Emeralds. Then, in the Shanazar arc, Robotnik work for Princess Kupacious as Grand Vizier. Both times he was using them to furtherhis own goals, and he was a far greater threat than Princess Kupacious.
Hellraiser: Bloodline. After Angelique summons Pinhead to help her with John Merchant they stand on roughly equal ground. When Merchant tricks them he drags her back to Hell for her failure and makes her a part of his retinue of servant Cenobites.
Brokenstar was the Big Bad of Into the Wild, the first book of the Warrior Cats series. Then he gets driven out of his clan and killed, leaving Tigerstar in control of his army. Later in the Omen Of The Stars arc, Tigerstar and Brokenstar meet up in the afterlife and Tigerstar becomes Brokenstar's dragon.
Caine Soren is reduced to this briefly during HUNGER (the first of many sequels to GONE). He bounces back though.
Happened in the backstory of the Chronicles of Thomas Covenant. The three Raversnote Moksha Jehannum, Turiya Herem and Samadhi Sheol (formerly human, bodiless possessing demons) were the Land's reigning supreme evils for centuries, possibly millennia- at least until Lord Foul the Despiser showed up to seize the throne of Big Badde jure. In the process, he made the Ravers his chief minions (an arrangement which worked out well for the Ravers; Foul was as evil as they were, far more powerful, and an extremely subtle chessmaster, so allying with him made them if anything even more dangerousnote and they think they'll get godhood themselves when Foul busts free of the Arch of Time, though it's unclear if Foul can actually deliver this). However, by the time the actual books take place, this is entirely a matter of legend; the Ravers are well-known primarily as Foul's minions, and are even described as such in the books' glossaries.
Angel: A variant for the good guys — after Angel has a Heroic BSOD and fires everyone in Angel Investigations, he gets better and asks for them to return, as his bosses not his employees — he demotes himself to Dragon. Eventually he goes back to being the boss but it's never quite established how. It's because Wesley betrayed the team's trust in a misguided attempt to protect Angel's son, and was subsequently booted from being the boss of AI later in Season 3. He later returned, but stayed as The Smart Guy. And really, from that point on everyone had their own role on the team, with nobody being 'in charge' again until Season 5, when they took over Wolfram and Hart.
A strange variant in Smallville's Season 10 episode, "Dominion". General Zod, the Bigger Bad of Season 5, and Major Zod (his clone), the Big Bad of Season 9, were fused into a single being by Darkseid, the Season 10 Big Bad, and used as his surrogate in the Phantom Zone.
Darken Rahl is the Big Bad of the first season of Legend of the Seeker. Then he's killed in the season finale. Come season 2, the Keeper has become the new Big Bad, seeking to kill every living thing, with the Rahl's soul being his Dragon. Not only that, but he reveals that he has always served the Keeper after making a Deal with the Devil for more power, and all his murders and slaughters were partly to appease his master. Then again, Rahl is a dick either way and really enjoyr killing. Of course, he turns out to be a Dragon with an Agenda and betrays his master by the end. Additionally, in the episode where Zedd's spell goes awry and rewrites history, Rahl becomes Richard's willing assistant, after Richard brainwashes him. Then the spell is broken, and Rahl is back to his old self.
Farscape: Crais briefly experiences this once Scorpius deposes him as captain of his Peacekeeper battleship, but takes the first opportunity to desert and do his own thing.
Done briefly in Stargate SG-1. Initial Big Bad Apophis is hunted down by replacement Big Bad Sokar and dies while hiding on Earth. In a later episode, one of the lesser Goa'ulds serving Sokar has a First Prime named Na'onak who turns out to be a regenerated Apophis in disguise. However, Apophis rapidly pulls a Starscream on both and reclaims the Big Bad throne.
The Undertaker, as the leader of the Ministry of Darkness, was clearly seen as the biggest threat in the WWF at the time, to the point where it seemed even Vince McMahon was getting face cheers over him and was being portrayed somewhat sympathetically. However, Taker began making references to a "Higher Power", and when it was time for the reveal, it was none other than McMahon himself who had been pulling the strings all along. The Ministry merged with The Corporation to form the Corporate Ministry, and Undertaker immediately became McMahon's dragon.
In Super Mario Land. Tatanga is the Final Boss. In the sequel, Wario is the Final Boss, and Tatanga is simply guarding one of his coins for some reason. It's implied he may have been working for Wario the whole time, given that Wario takes over when Mario was distracted by Tatanga.
Happened to Lechuck in Escape from Monkey Island, though he does turn on the game's new villain in the endgame when they're defeated.
In Final Fantasy X, the seemingly Big BadFinal Boss called Sin turned out to only be an armor used by Yu Yevon, the center of the world's only religion and pretty much their god. From the moment the cast learns this, Sin is technically Demoted to Dragon, because the player had expected that Sin/Jecht would be the Big Bad.
Medusa, the villain of the first Kid Icarus game, is actually reduced to this in Kid Icarus: Uprising. Though in what may have been an Author's Saving Throw in case this wasn't well received, it's revealed that the Medusa in Uprisingisn't actually Medusa, just a whole bunch of random souls Hades put together in a Medusa-shaped container.
In the arcade version of Double Dragon, Machine Gun Willy is the leader of the Black Warriors and the final boss in the game. In the NES version, he's simply the last guy the player must face before the final battle against the player's twin brother, who became the main villain in the NES version. Note that while the sibling battle also occurs in the arcade version, it was an optional fight that only occurs if two people were playing, whereas in the NES version it's mandatory to completing the game.
The Magician reappears in House of the Dead 2 as the penultimate boss before the final stage. He isn't any easier to beat, though. Probably doesn't count though, since he isn't related the the bad guy's plan at all. He's a Giant Space Flea from Nowhere.
Also happens to Geese Howard in Fatal Fury Special, where he is the last opponent the player must face before facing Geese's half-brother Wolfgang Krauser. In Real Bout Special, it happens the other way around.
In the Genesis version of Golden Axe, the player must face Death Bringer (a console-exclusive final boss) after defeating Death Adder (the final boss in the arcade version).
As of Kingdom Hearts 3D: Dream Drop Distance, Ansem, Seeker of Darkness and Xemnas, the Big Bads of the first and second game, respectively, have both been Demoted To Dragon under Master Xehanort (either that, or Master Xehanort was playing the Man Behind The Men the entire time) For the record, these are all different incarnations / versions of the exact same guy.
The second Ninja Gaiden game for the NES managed to pull a double dragon demotion.. Jaquio, the big bad of the first game, is revealed at the start of the sequel to have just been the dragon of Ashtar, the true Big Bad who had been pulling the strings all along. But then Ashtar ends up dying halfway through the game, and the player spends the second half wondering who's really in charge. Turns out it was Jaquio all along. Ashtar was actually the starscream of Jaquio's organization, so Jaquio let Ashtar think he was in charge so he'd stick his neck out and get killed by the hero. It worked, and as a result Jaquio is more powerful than ever.
In Battle Clash, the space alien Anubis is the last boss of the game. In the sequel, Metal Combat, it is revealed that Anubis was following orders from a race of alien invaders who were plotting to conquer the Earth as a replacement for their lost home.
In Harry Potter Comics, Voldemort is revived by a mysterious Necromancer for the sole purpose of being his Dragon (and fully opening the Chamber of Secrets).
On Atop the Fourth Wall, Mechakara was the Big Bad starting from the May 2009 episodes. After the storyline concluded in February 2010, Mechakara later reappeared as The Dragon to the new Big Bad, Lord Vyce. Unlike other cases, Mechakara doesn't suffer from Villain Decay, becoming more of a threat due him being upgraded.
The Trix from Winx Club were the main villains in season 1. In seasons 2, 3, the 2nd movie, and 5 they work for the more powerful villains Lord Darkar, Valtor, the Ancestral Witches, and Tritannus.
In G.I. Joe, this happens to Cobra Commander when Serpentor is created.
Slade from Teen Titans is demoted to Trigon's dragon when the latter tries to take over the world. An unusual case where the former Big Bad is actually more of a threat to the heroes when he's serving as someone else's henchman, because Trigon gave him a truckload of powers in the bargain.
Shendu, from Jackie Chan Adventures. For the first season he was the one calling the shots but after his defeat he is forced into servitude to his demon siblings. Though in this case, he demoted himself so they'd stop beating the crap out of him for leaving them to rot in their prison.
In Danny Phantom the Fright Knight became Pariah Dark's Dragon when he awoke. Though in this case, the Fright Knight was always Pariah's Dragon, his boss was just Sealed Evil in a Can when the Fright Knight was unleashed the first time. Vlad convinced him to turn against his master offscreen.
Transformers Prime: This is played with when Unicron shows up. Megatronwants to serve him, but Unicron doesn't give a crap about Megatron, viewing him as beneath him. Which is a total reversal of the G1 situation ("serve me or get eaten") and the Transformers Armada situation ("you've actually been serving me all along.") where it's an unwilling Megs being made to work for Unicron until he can turn the tables. (If you go with the All There in the ManualRetcon that there's just one Unicron, it could be that the Chaos-Bringer has just learned that Megatrons don't make good servants.)
They do cross paths again in the finale movie. He still doesn't become Unicron's dragon. Megatron's dead body is hijacked by Unicron, and Unicron proceeds to torture Megatron whenever he speaks out of turn.