As the page quote illustrates, Jokerella has the dubious distinction of being the least competent member of Wonderella's rogue's gallery. As Wonderella herself says on the cast page: "Jokerella would be The Little Villain Who Could if she could do anything."
The Dark Warriors in 8-Bit Theater. Ostensibly the greatest adversaries to the cast, they are considerably less threatening than the Fiends, who have consistently proven themselves to be dangerous, or the Light Warriors, who are probably one of the worst things to befall their world (with the possible exception of King Steve).
King Steve is a scourge to his citizens and the nations he goes to war with, but the Light Warriors? No one is safe from them.
Adventurers!! is so full of harmless villains that it would be easier to list who isn't one.
Well, under non-harmless villains there's Eternion and...uh...Argent's more of an anti-hero, so...just Eternion?
Demon-Jame in Terror Island, at least in his first series of appearances:
Demon-Jame: Are you enjoying your suffering, mortal? Aorist: What? Demon-Jame: Your crops. I blighted them. Aorist: I don't have crops. I have weeds. Did you blight my weeds? Demon-Jame: Um. Yes.
Completely undone in his second appearance, though. When he first shows up again, he spends a moment thinking about what evil plots he could do. Aorist jokingly suggests that he blight his weeds again, so Demon-Jame rips him in half.
The Minion Master from Sluggy Freelance isn't really interested in doing anything bad; he tends to view making people his minions as a way of helping them escape their old lives, more than anything else. And he doesn't even get any minions until Torg and Co. join him, at which point, they promptly start using his resources to battle evil, placating their "Master" by explaining that, as the big picture guy, he doesn't need to know the specifics, or anything at all, about what his minions are actually doing.
Wilson and Pickett from Notfunny Cartoons. Sure, they sell a large variety of killbots and genetically engineered killer werewolves, but they all range from being harmless to actively doing good (case in point, one of the killbots works as a kindergartener). They did make a highly-efficient killer virus they regularly deploy through their time machine, but only to make sure that the dinosaurs stay extinct. After a quick brainstorming session about what nefarious purposes they could use their time machine for, the best they can come up with is using it to sleep in on weekdays. It's not that they're reluctant mad scientists - they're just not very good at being evil.
However he is the son of the devil. So that could change. Then again Amnesia may change it the other way.
Horris from Zoophobia seems to be this, though that may change.
Pharaomoan from Essay Bee Comics Presents Fusion. While his power of using pheromones to control the behavior of men (just men, not women) in a 100 yards radius around him could make him a legitimate threat (imagine if he walked in an army base and recruited all the soldiers in under 10 minutes for any agenda), not only is he just a teenager in love with a girl who won't give him the time of the day because he's too much of a nice guy and only strolled around town gathering a small army of civilians just to "prove" he was bad, and he can't go through with making them do anything more since he doesn't want anyone to get hurt or get in trouble, but to push him even further into harmlessness, the Enigmatic Empowering Entity that gave him his power would have none of it if he turned evil.