The Clockwork King in City of Heroes is probably the closest it gets to Harmless Villain. The worst he might do to normal civilians is send his minions to steal a watch and some scrap metal, or make a mechanic work on his robots. He hates heroes, but given that a hero smacked him around so hard that he turned into a brain in a jar, that's probably justified. Turned slightly to the side of good with the Faultline revamp and his protection and assistance of some civilians, although the crazy kinda gets in the way of helping.
Super Mario Bros.: Mario's rival, Wario, in the Mario Sports games, as well as his partner Waluigi. They mostly just act like jerks while trying to ruin Mario's day. Wario was considerably more threatening — downright scary, even — in Super Smash Bros. Brawl's story mode, though still comical.
Wario has even been made a fool of in a game where he's the star. In Wario Land Shake It! his longtime rival Captain Syrup helps him for most of it, but in the end, she double-crosses him and robs him blind.
Pete, as characterized in Kingdom Hearts, is a bumbling oaf who never inflicts any lasting harm on either the characters or the worlds they fight to save, as opposed to Maleficent, who, in the first game, turned the main character and his best friend against one another and led them all down the path that would separate them and the girl they were fighting over for several years, and was likely responsible for the destruction of several worlds. This is also in contrast to his characterization as the Ghost of Christmas Yet to Come in ''Mickey's Christmas Carol', nearly two decades earlier, where he laughed diabolically as he unmasked himself and sent Scrooge falling into the fiery pits of hell.
The tougher Pete is more or less the original concept of Pete, who's often as tough as ever when battling Mickey, Goofy, and others in the comics (even today). He clearly thinks nothing of trying to kill our heroes with swords, guns, clubs, and other weapons, and often is only stopped by dumb luck. Or by Mickey Mouse in rare Badass mode, who, while much smaller than Pete, is a fast and clever (if comedic) fighter.
Murray, the Mighty Demonic Skull from Monkey Island. Since Guybrush sort-of-accidentally smashed his body with a cannonball, he's stuck as an immobile skull with a great desire for evil and absolutely no capacity whatsoever to indulge it. He's kinda bitter.
Mysterio, the Spider-Man 2 game version. Sure, he's got like a million robots and can successfully kill people from time to time, but man, what a friggin' loser. And he's got a glass jaw.
Kirby's arch enemy, King Dedede, depending on the game. The most evil deeds the king performed without being possessed by Dark Matter was stealing the stars from the sky and stealing food from Dream Land for the hell of it.
Wheatley in Portal 2, when he becomes evil after being plugged into the mainframe of Aperture Science. He does pose a genuine and intentional threat...briefly, twice. The rest of the time he's dangerous not from menace but sheer idiocy, his complete incompetence at controlling Aperture Science threatening to destroy the facility in a nuclear meltdown. It turns out he has a reason for being such an ineffective villain: Aperture literally designed him to be stupid so that they could attach him to GLaDOS to keep her from becoming dangerous.
The Defective Turrets also qualify. They sound very enthusiastic about killing you, but unfortunately for them, they don't have any bullets.
In StarCraft II, Donny Vermillion likes to fancy himself as the face of Emperor Mengsk's unstoppable Propaganda Machine. In truth, he's laughably incompetent at his job; the fact that his star reporter either isn't in on the plan or actually likes Raynor doesn't help. Supposedly, the media is a major weapon for Mengsk, so it's possible Raynor only watches Donny's show because the others are actually good at it.
The Fallout: New Vegas DLC Old World Blues has The Toaster, an Omnicidal Maniac obsessed with burning the world. He is limited in his evil quest by being a talking toaster (and that alas, unbeknownst to him, the world has already burned. He gets very upset if you happen to point this out). About the worst he can do, should you not suffer an attack of stupid and stick your hand into his bread slot, is threaten to set you on fire. He is a substantial danger to other toasters, though - provided you bring them to him.
Okage: Shadow King has Evil King Stanley Hihat Trinidad XIV, or Stan, the Sealed Evil in a Can who's taken over your shadow. He really likes proclaiming how evil and mighty he is, but with one of his first displays of his terrible might being to rescue a cat stuck in a tree, he is not that good at it. Especially with how a bunch of Fake Evil Kings have stolen his power while he was sealed away.
Played for laughs in The Elder Scrolls series. In Oblivion, you fight the very villainous and not-at-all harmless MythicDawn Daedric cult, which almost manages to destroy the world. Then, a few centuries later, the Player Character in Skyrim can meet a half-crazed fanboy of the Mythic Dawn who collects their old books and ceremonial garments, runs a Mythic Dawn Museum, and dreams of reviving the cult. He's serious about it but laughably incompetent and absolutely nobody takes him seriously except Mehrunes Dagon, Daedric Prince of Destruction and former patron of the Mythic Dawn, who doesn't really like clueless wannabes exploiting the heritage of his most devoted and successful servants.
Fallen London: In just about any other setting, a series of highly like-minded Ax-CrazyKnife Nuts who like to hide in snowmen to ambush people and just generally love to slash throats and cut people up would be a very dangerous sort. In a setting where Death Is Cheap even to the poorest commoner (to the point some Londoners murder each other for fun), and Slashed Throat victims can get up minutes after he's left, Jack of Smiles, formerly known as Jack the Ripper, isn't given anything even close to respect.
Veigar in League of Legends is so bad at being an Evil Overlord that he generally ends up providing a net benefit to the people he attempts to oppress, since he may end up overthrowing an actually effective villain or taking out some dangerous predators or blowing up a bandit outpost on his way there just out of orneriness.