Narbonic centers around Dave Davenport and his employer, the Mad Scientist Dr. Helen Narbon. Dave's fully aware of what Helen does for a living and will occasionally note how odd it is that none of it fazes him. Maybe if she succeeded more often...
A dominant theme of the webcomic Evil Inc.. Several of the protagonists have "mixed marriages" (that is, hero/villain), some of which are kept secret in the interest of comedy.
Kroenen, and, to a lesser extend, most of the bad guys in Abe Kroenen. However, with the death of Rasputin, most of his minions seem to be rather depressed not to have someone boss them around.
After they (temporarily) destroy Xykon, one of his remaining minions announces that, since nobody is paying them to fight anymore, they're surrendering. Unfortunately, he announces this to Belkar, who, undaunted, proceeds to wholesale slaughter the "pretty little chunks of XP". They are speaking the truth, too. As shown in the Start Of Darkness prequel, Xykons goblin-minions were given the choice to "join or die".
Again, in The Order of the Stick, comics 30-32 take place in the secret Break Room of Xykon's Lair, where they encounter a "squid-thingy" before the comic is interrupted by two Lawyers sent to prosecute the comic for violation of the Open Gaming License.
While Therkla has an Undying Loyalty to her master Kubota, she doesn't really care about the politics involved. She attempts to assassinate Hinjo only because that's Kubota's order (which is stopped by her falling in love with Elan, eventually leading to a Heel–Face Door-Slam).
Much later on the series, the Order meets General Tarquin, Elan's father. While he has his reasons for wanting parts of the Order dead, his followers, Laurin Shattersmith and Miron Shewdanker have nothing against the Order, and don't even want to get involved, Tarquin calls in a 12-year-old favor to get Miron on board, and Laurin uses the situation to get a favor of her own.
Debatable in Kevin & Kell. Kell's job is to hunt and eat herbivores, but she's also married to one. Makes you wonder why she doesn't change jobs.
Most of the Combine in Concerned, as well as their few human employees (including Gordon Frohman himself).
In Terinu, the Big Bad's chosen leader for his genetically created group of minions is a happy family man who's concerned for his pregnant wife, who just happens to leads invasions of innocent worlds for his master.
Since then, Fuschia has left Big D's employ entirely, and is trying to re-invent herself as an artist.
Subverted in Scary Go Round, where "evil intern" Gibbous Moon returns to romance Ryan, and turns out to be the field general for a crew of pirates, disguised as Blackbeard's ghost.
The major thematic element of Chopping Block. While Butch certainly enjoys what he does, he views it very much as a job, trying to make quotas, keeping a professional standard, and occasionally talking shop with other killers (though he detests that).
Abraham from El Goonish Shive seems to be this. He takes no pleasure in what he does, and it's heavily implied that if it wasn't for his oath, he wouldn't be antagonizing the cast, but he lacks the openly sympathetic aspect that would make him an Anti-Villain.
This Arc of Jack deals with the ethical dilemmas of a person finding themself an unwilling punch clock villain by discovering half way through their employment that their boss is a monster (specifically, a twisted paedophile), and being unable to quit or tell anyone because he's also weeks from finding a cancer cure for his wife's terminal cancer.
Gen. William Howe in The Dreamer. He really doesn't want to fight against the very people he fought with in the French And Indian War, but he has no choice but to follow orders.
In-Story, Jack Noir/Spades Slick would be this for any SBURB session, being a Dersite government official, and later attempting regicide and being exiled. In the Kids' game, him actually succeeding is what sets the campaign Off the Rails.
In Sidekick Girl, Coldfire is a henchman who only henches because his visa is tied to the Henchman Agency, and he has a bounty on his head back in his home country. He often willingly helps the heroes in secret.
In Nintendo Acres, villains like Bowser, Ganon, and Dr. Eggman, like almost everyone else, are simply actors who work in video games, and are actually quite nice people.
In Voodoo Walrus, Shmeerm seems to exhibit qualities of this. If he doesn't have express orders to pummel, eviscerate, and destroy people, places, and things, he seems content to simply traumatize catgirls and talk about his relationship problems with a science badger over tea.
Sentry of Ask-a-Sentry, a Tumblr-based Tron webcomic. He's a sweet, awkward guy who just happens to be a member of Clu's army, and who wants nothing more than to fulfill his directives to the best of his ability (when he's not getting distracted, that is...)
Mephistopheles and Adramelech from Underling. The former is Hell's bookkeeper (and dresses the part), the other is an old, washed-out god who resents having been forced to join The Legions of Hell by the rise of monotheism (he still does his job, though. Except no.
Major Murtaugh and the rest of Sanctum Adroit from Book 12 of Schlock Mercenary. They may be fighting against the Toughs, but they are fundamentally good people who are just trying to maintain peace and order.