Repo! The Genetic Opera has Amber Sweet. She's just as nasty as her brothers, but she's usually too high on zydrate to be effectual.
And Luigi and Pavi aren't much better, given that Luigi, despite his claims that only he's got brains enough, comes across as a simple minded Knife Nut and Pavi spends most of his time staring at his own face in the mirror he forever carries with him. That being said, Luigi is quite effective in the "stabbing people for no good reason" compartment, which makes him the least harmless of the Largo siblings.
Justin Hammer in the live-action Iron Man sequel pretends to be an Evil Counterpart of Tony Stark, but is an ineffectual clown whose products are very poor quality, whose attempts to intimidate the actual villain of the movie would work better on a five-year old, and whose henchmen are incompetent rentacops who carry mace and tasers.
Doctor Evil from Austin Powers. "Here's the plan: we get the warhead, and hold the world ransom for...ONE MILLION DOLLARS!"
On the other hand, he does win several ransoms and come pretty close to destroying the world. He's even killed people, including Felicity...at first.
Of course, the whole ransom thing was more to do with misinformation about global economics after his cryosleep than with being particularly harmless. When he tried to extort $100 billion after returning to the sixties in the second movie, he gets laughed at because that kind of money didn't exist back then. He seems to get the hang of things by the third movie, where he demands a ransom with a number that doesn't exist, but in Yen. The UN doesn't dispute it, considering it a more or less reasonable demand.
Scott Evil is very much this. He just can't quite be villainous enough to fit in with the rest of the villains, at least until the third film.
Dr Evil:(while talking down to Scott) You're the diet coke of evil. Just one calorie. Not evil enough!
Regarding Scott, it's probably not so much a lack of villainousness that prevents him from fitting in as a lack of Contractual Genre Blindness.
"Cactus" Jack Slade from the western parody, The Villain.
In Zombie Blood Bath, the zombies seem to be relatively harmless so long as you don't just stand there and let them kill you. In one scene, they had to get pass an army of zombies on a staircase, and they did this by...just gently shoving them aside. The zombies groaned and flailed their arms, but didn't seem to pay much attention to them.
William Bludworth in the Final Destination films only serves two functions: to play the part of Death's own personal janitor, and to give the protagonists cryptic clues on how to evade death for as long as they can. Even when Peter takes his advice to "kill or be killed" way too far, that's a matter of responsibility on the part of he who hears the advice, and the other two who use the "kill or be killed" tip aren't nearly as monstrous as Peter was: Nathan uses the advice completely by accident when Roy gets impaled by a hook during a confrontation over a rude remark directed at the former, and Sam uses Bludworth's words responsibly by killing Peter to prevent him from murdering Molly.
Connor from The New Guy. Most of his scenes he constantly gives insults that don't make sense. When his friends point this out he always tells them to "shut up". Doens't help that in one scene, he is knocked unconsious by Dizzy, who looks phsyically weaker then him.