On the Neopets website, Doctor Sloth's Dragon is Commander Garoo, although he hasn't enjoyed much screen time.
In Survival of the Fittest, the main Dragon to Danya (although he has a number of prominent henchmen) is Steve Wilson, who was effectively in charge of orchestrating a whole slew of the kidnappings which comprised Version 2 of SOTF. However, the three other members of the so-called "Big Four" — Jim Greynolds, Melvin Carter and Sonia Nguyen — could each be considered a dragon in their own right; it's up to interpretation who is the official right hand man.
In Protectors of the Plot Continuum, Nendil MorifŽa was the Bracket Fungus's Dragon before and during their invasion of HQ, and may have eventually taken over the Black Cats afterwards if things had gone differently; the BF himself could have been said to be The Dragon to the Mysterious Somebody, during the latter's reign as head of the PPC. The head of the League of Mary-Sue Factories has multiple Dragons in the form of their lieutenants, themselves usually the heads of their own Mary Sue Factories. The current Big Bad, the Venomous Tentacula, is a Dragon Ascendant, as he'd been one of the Yarrow's lieutenants and won an Enemy Civil War to replace him. Finally, while it's not made clear, the Mirror Multiverse's version of the Mysterious Somebody seems to have this role for the Sunflower Emperor.
Major Shaun Wendelferce from E.H.U.D.: Prelude to Apocalypse starts out being just a side of the protagonist's love triangle, but the later chapters firmly establish him as the dragon, especially in the flash backs. Bonus points for having a Freudian Excuse for being evil.
The Slender Man will sometimes use one, such as Albert Conaghan in Seeking Truth. In Marble Hornets, it's initially implied that totheark is this, but by the end of Season 2 it's fairly clear that totheark has his own agenda while the role of Dragon belongs to Alex.
In The Gamers Alliance, there have been quite a few right-hand men and women serving various villains.
Brownie is this to Toki in any of any sort of stories where Toki is playing an antagonistic role and she does almost whatever Toki tells her without question. One could basically define the two as master and dog, literally, as Brownie is an anthro dog and acts as dogs do.
Contessa (from the web serial novel Worm) is Doctor Mother's closest, longest-standing and most effective subordinate, although, as seen in her Interlude, they formed Cauldron together. Contessa eventually just let Doctor Mother call the shots while Contessa focused on finding the paths to success with her power.