Dr. Robotnik on the Adventures of Sonic the Hedgehog version of the show makes incredibly inept robots, repeatedly has crying fits, and is sometimes too distracted with himself to notice that his plan isn't working.
It is also worth noting that Robotnik purposely made his robots dumb, so they would be too Incompetent to ever consider betraying him.
Note that in the SatAM series that was aired around the same time, Robotnik is...very much not harmless. At all.
Bling-Bling Boy in Johnny Test. Johnny is both his archenemy and his only friend. Most of his evil ambitions are done solely for the purpose of getting a date with Susan.
Petey Pate from Mighty Mouse: The New Adventures is a weak villain because most of the people from Mouseville make fun of him for his...well...just look at him.
Dr. Drakken in Kim Possible is pretty much the mascot of this trope, if only because that show's Periphery Demographic makes it so self-aware. You get the feeling that he and Shego aren't even trying to harm Kim, just keep her occupied. He becomes a Not-So-Harmless Villain in some cases, especially in The Movie "So the Drama". (In fact, being the most recurring villain, he's all over the scale; sometimes he's so ridiculous that Kim hardly needs to bother, but he's also the one who occasionally comes closest to his Take Over the World goal.) Occasionally he's not so much harmless as dangerously incompetent, his plans having a tendency to go horribly right or wrong.
This is because Drakken is an Expy of Doctor Evil, with Shego taking Scott's place as the more competent one who points out the other's ineffectiveness with snarky remarks.
Many villains on the show could seem like this. Senor Senior Senior and Senor Senior Junior probably take the cake, though, since supervillainy is just a hobby for them and they are kind of amateurish at it, being threats only because they are so ludicrously rich that they can actually afford their ill-though out schemes. Junior doesn't even want to be a villain in the first place.
Swiper in Dora the Explorer: any villain who can be foiled by saying "Swiper, no swiping!" isn't going to give Hannibal Lecter a run for his money.
Oh, and when he gets the stuff? Does he keep it for himself? No, he throws it into the bushes with a cackle of, "You'll never find it now!" and runs off.
There's even the Moral Dissonance that occurs during "The Berry Hunt", in which Dora and Boots sneak onto a hill where Swiper lives, quietly lift a bucketful of berries, then make enough noise that Swiper comes out of his hole...and the heroic duo frown at the thought that Swiper might steal "their" blueberries. "That Swiper!"
There was an episode where he stole the friendship bracelets for friendship day. When he found out, he did a Heel-Face Turn for the rest of the episode and helped the rest of the cast find all the bracelets.
There was also the Christmas Special, where Dora and Boots took a trip to bring a present for Santa. Along the way, Swiper swipes it, but does a Heel-Face Turn and returns it when he's told what he had taken.
Glowface from The X's is one such villain. He even gets upset when his monologues are interrupted, and is perfectly willing to put off villain chores to play video games.
The Monarch in The Venture Bros. almost qualifies. When he isn't psychologically damaged, being pushed around by the higher-ups in the Guild of Calamitous Intent, and being inept at commanding his henchmen, he can, in fact, be quite deadly. The trouble is, he's so bad at arching that his nemesis, Dr. Venture, doesn't even consider him a real threat. Later seasons show, however, that The Monarch can, indeed, be a very threatening villain, if he bothered to extend his goals beyond being a pain in the ass to Dr. Venture.
In season 3, Sergeant Hatred better qualifies for this trope. He signs up to be Dr. Venture's arch, but then resorts to extremely minor acts of villainy, such as lighting his front-yard shrubbery on fire. By the end of the season, he even lives on the Venture Compound and acts as an ad-hoc bodyguard in the absence of Brock Samson, who is working for an undercover vigilante society. Of course, he only did it to piss off The Monarch, who repeatedly stole tech from him.
There's also this exchange at the line for Order of the Triad archenemy try-outs:
Torrid: Hey, isn't that Doctor Venture's lab?
The Intangible Fancy: Yes, I believe it is.
Torrid: Save my place in the queue. There's something I feel I must do. Something...torrid.
After the commercial break, it's revealed that Torrid really meant using the bathroom.
When Phantom Limb is holding tryouts for his own supervillain organization, most of the people that show up are... well, it's no wonder the Guild turned them down. Brick Frog, indeed.
Duke Igthorn in Adventures of the Gummi Bears was mostly cartoonishly harmless. At one point, he had captured Granni Bear, and was trying to extract the recipe for the Gummi Berry Juice from her. Rather than torture, he actually tickles her with feathers until she gives in. Thankfully, it was an incorrect recipe, proving that the Jack Bauer Interrogation Technique (with feathers) is still useless. However, if one looks deeper, one can gain some respect for the man; he seems to keep a legion of superstrong ogres twice his size in line by mere force of personality, is never seen not wearing a suit of chainmail (which is HEAVY), and, at one point, knocks out two armed guards with his bare hands.
It's also clear that if it hadn't been for the Gummi Bears, he would have taken over Dunwin a long time ago. Even if most people now believe that the Gummi Bears only are fairy-tale characters, they remain a threat to Duke Igthorn, that the king's knights only can dream of being. And there's also one episode, where he blows up a tower and could have killed Princess Calla (she even was unconscious for a while). So yes, Duke Igthorn sure had his dangerous moments.
The Box Ghost ("Beware!") from Danny Phantom certainly qualifies as the resident Harmless Villain, who gets little to no respect from Danny and the other evil ghosts alike. However, his threat level mainly depends on what the boxes he uses to fight with contain.
Since the Box Ghost (apart from that time with Pandora) never seems to have plots more complicated than "throw stuff around to scare people", Danny's probably just being a bully by attacking him at all.
The Amoeba Boys in The Powerpuff Girls. Their devious plans include crimes such as disobeying a "Keep off the grass" sign (*gasp*), jaywalking (*SHOCK*) and...dare we mention it?...Littering (*DUN DUN DUN*). They only turned to such crimes after they tried, and failed, to work up the courage to steal an orange from a produce stand.
Hilariously, the "Keep off the grass" thing turned into one of the most serious threats in the show's run. The Amoeba Boys stayed on the grass all night, through a storm, and got colds. As they are gigantic germ...things, this mutated into a disease that could have killed off all of Townsville if the Girls hadn't managed to find the Amoeba Boys and convince them to let a vaccine be extracted. Of course, absolutely none of this was intentional, but hey.
They almost crossed the line to Not-So-Harmless Villain in one episode, where they were able to create an army of duplicates of themselves using mitosis, and then stole all the oranges in Townsville, resulting in almost all the populace getting sick with scurvy (a clear-cut case of Rule of Funny). It was rather easy for the Girls to beat them to a pulp, but in the end, that was what they had wanted all along.
They also sent the Girls voodoo dolls they had made to torment them with as a birthday present. When the Girls are opening their presents, they see this one marked "From The Ameoba Boys" and are assured by the Professor that the Boys can't do anything right, so the present must be safe to open.
And yes, you read that right. They sent the voodoo dolls to their targets. When Mojo Jojo points out that's not how it works, they're completely baffled.
The Powerpuff Girls Z version of the Ameoba Boys has a better grasp of how to be villains, but since they're just barely visible to the naked eye, it's impossible for anyone to take them seriously.
In "Supper Villain", the Girls' next-door neighbor Harold Smith gets bored with his mundane suburban life and becomes a supervillain, holding Professor Utonium hostage with a ray-gun made from a hair dryer. He's thwarted first because his wife insists they finish dinner first, and then by a pie fight.
He does get at least one Not-So-Harmless Villain moment in the series, in which he gets a hold of another lamp and wishes that the protagonists get smashed like bugs. When told that genies can't kill, he has a moment of brilliance and asks for the protagonists to be turned into bugs so that he can smash them like bugs.
He also went back in time and rewrote Agrabah's history in one episode so that he could be Sultan.
Aladdin also occasionally had to deal with an inept thief named Amin Damoola (nicknamed "Butterfingers"). The only time Butterfingers was a serious threat was once, when was using magical artifacts supplied by Mozenrath, who had essentially replaced Jafar as Aladdin's main nemesis.
Doctor Light in Teen Titans seems more like the team's punching bag than their enemy.
He doesn't come across as all that harmless so long as Raven isn't around; in his introduction, he's actually winning against the Titans and usually puts up a pretty good fight until Raven talks to him and he falls apart. If she wasn't around, he'd be anything but harmless.
In Xiaolin Showdown, Jack Spicer pretty much fits this trope, to the point where other villains used his name as a slang term to describe this trope. Jack-Bots, indeed.
Like others on this list, he becomes a Not-So-Harmless Villain in an alternate future. Without Omi messing up his game, Spicer steals all the Shen Gong Wu, traps the other Big Bads in humiliating circumstances, and conquers the world. His Jack-Bots are upgraded to Humongous Mecha and he himself uses Powered Armor that incorporates at least two Shen Gong Wu in its design. Before Omi is able to go back in time to fix things, Spicer actually kills the other Xiaolin Warriors, albeit offscreen.
The villain Killface from Frisky Dingo is a good example. He builds a machine that can destroy Earth but freaks out and tries to stop it when someone activates it. He also shows some love for Earth, especially its pre-Colombian pottery and literature (but not the hip-hop). He becomes best friends with his worst enemy (who is disguised) and refuses to kill him, even after finding out his true identity. He has no problem brutally killing his "employees," though. The hero, Xander Crews, actually does more evil and harmful things than Killface.
Phineas and Ferb has the completely harmless Dr. Doofenshmirtz. The closest he came to actually harming anyone was building an invention that would destroy anyone who couldn't make up their minds.
In his defense, he's facing a badassplatypus who simply hand waves all of his crazy plots with that awesome purr/growl sound of his.
The man was once defeated by a potted plant he hung up because Perry was busy. It doesn't get any more harmless than that!
Most of his plans are self-foiling, though. They ultimately fail even when Perry never shows up, such as in the aforementioned plant episode.
All of that said, "Phineas and Ferb's Quantum Boogaloo" shows us that without Perry to oppose him, he can be much more dangerous. (Granted, that was a unique situation, since it's implied that the citizens of Danville asked him to rule them out of fear of their own children.)
One episode had him cloning himself not to make it easier to take over the Tri-State Area, but so he could get errands done quicker such as standing in line.
Professor Esmeralda Poofenplotz (Pinkie the Chihuahua's nemesis) is even worse; Her first appearance revolved around finding a stash of her favourite discontinued hairspray (as she felt she couldn't commit evil without good-looking hair), and the second involved a poorly thought out plan to eat enough royal jelly to turn herself into a queen bee. Even Doofenshmirtz considers her to be a harmless villain (to the point where he didn't allow her to join his evil organisation L.O.V.E.M.U.F.F.I.N.).
It's pretty hard to bring oneself to hate any of the villains in the Scooby-Doo cartoons, because most of the time, their idea of an evil scheme was to put on a monster costume and chase a bunch of hippies and dogs around. Not to mention, nearly all the time, the motive is to "scare people away" for some reason or other, but never kill.
There was one episode where they unmasked the villain and were all like "You're going to jail!" only for a police officer to inform them that, seeing as she was on her own property, not actually hurting or threatening anyone, and not covering up for any sort of criminal operation, she hadn't actually broken any laws and so she wasn't going to jail.
One villain in What's New, Scooby-Doo? pretended to sabotage a bunch of carnival rides out of jealousy for her sister. They managed to unmask her, but because the rides hadn't actually been sabotaged and she hadn't otherwise broken any laws, they had to let her go.
This has been averted in Mystery Inc. as the villains are much more willing to kill, or at least maim, the gang. One even tried arson to stop the door gag. No wonder this Shaggy hates mysteries.
On the original series, they weren't out to hurt anybody; almost every one of them was involved in some kind of ludicrous real estate scheme where they really, really wanted to have the rights to some particular land/house, and thought the best way to do that was to put on a monster costume.
Codename: Kids Next Door has the Toiletnator. He is as threatening as he sounds. Not only is he harmless to the heroes, his incompetance can be detrimental to other villains; Mr. Boss once alluded to an incident where he let Numbah One into the villains' secret lair when Numbah One's only disguise was a t-shirt with the words "I am not Numbah One" written on it. This becomes a Double Subversion when he actually becomes competent in one episode - but destroys his own side with his stupidity.
The Toilenator is so pathetic, he can't even claim the title of Best Toilet-Based Villain. In "Operation: A.W.A.R.D.S." He was nominated for the title in an awards ceremony held by the other villains, but lost to Potty Mouth.
There have actually been several episodes that show that he isn't so harmless, it's just that he really isn't that evil.
"The Villain Nobody Took Seriously" on The Secret Show, who was able to rule the world precisely because nobody took him seriously. He was just a clown living in an abandoned circus tent, talking about all the things he would do once he ruled the world...and then managed to get elected World Leader by changing his name to "Mark X Here", making confused voters cast their votes for him.
All of them, however, have to be topped by Wile E. Coyote, the epitome of the villainous Butt Monkey.
And Sylvester prety much defines this trope.
The League of Super Evil. They not only Poke the Poodle figuratively, they might do so literally, claiming it to be a villainous deed. Which, considering that their previous plots include Voltar using a giant mech so he could play in a dunk contest, rigging a pet show to win, and selling turnip-ade under the guise of lemonade, might be a step up for them.
Strawberry Shortcake's Peculiar Purple Pieman of Porcupine Peak. In the first two animated specials in the first generation line, he floods Strawberryland to demand its berries as ransom, and cheats to win a bake-off in which the prize is a gazebo. With his associate Sour Grapes, their crimes in the subsequent four shows are: framing Strawberry for taking a bribe as a pet show judge and being complicit in their cheating, stealing a box of recipes, capturing a friendly monster with the intent of selling it to a circus, and trying to use the Berrykins to create a super-perfume. Sometimes, the real dangers to the heroes are unintentional on the villains' part: Lem and Ada are hiding in the recipe box, and the perfume mixing results in a smelly cloud that threatens to stink up Strawberryland. Also, as far as weaknesses go...in the third special, he crumbles under the heroine's threat to annoy him endlessly with her "berry talk".
In all fairness, you shouldn't underestimate the potential of a gazebo.
Evil Cosmo. Oh my god, Evil Cosmo. He's even a failure at poking the Cat.
In one episode of The Legend of Zelda, "The Moblins Are Revolting", Ganon's minions grow tired of doing his bidding and manage to get rid of him (temporarily), then conduct their own attack on Hyrule Castle. Link and Zelda don't even stay to defend the castle because it's not in any danger; the monsters wipe each other out in the process of trying to invade, and never get anywhere near the building.
In the Batman: The Animated Series episode Make 'Em Laugh we have the Condiment King, one of the comedians brainwashed into a villain by The Joker. He fights by squirting ketchup, mustard, and hot sauce which, amazingly enough, does manage to take down one restaurant patron and intimidate the rest into actually handing over their priceless valuables. Batman takes him down in one easy punch and, seeing how pathetic the guy is, actually offers to go easy on him.
Batman: Now listen, Mustard Man, or whatever you call yourself: you're obviously new at this so I'm willing to go easy on you, provided you give back the loot and don't even think about doing this again.
Played with in The Batman with veteran Bat-villain Killer Moth. As with his comics version, he started out as some weirdo in a costume. He later got transformed into a giant super-strong mutant moth with the ability to spit acid...but he retains his milquetoast personality, so he's really pretty easy to deal with.
Lucius Heinous VII on Jimmy Two-Shoes is pretty much an incompetent version of Satan. Though, while he's largely ineffective, the fact that he keeps people like Heloise and Molotov under his thumb is probably a sign that he's doing something right.
The Shredder in the Teenage Mutant Ninja Turtles 1987 TV series after the initial story arc of the first season. Only in that one though; the other media tends to show him as a real threat.
Finn, Ratso and Chow in Jackie Chan Adventures should qualify. While they are, most of the time, serving the Big Bads of each season, they serve, pretty much, as Jackie's punching bags. Even when Daolon Wong grants them demonic powers. In the only episode I remember them going solo, they even pulled a Heel-Face Turn (it didn't stick, though)!
Mostly because they were just as bad at being good as they were at being bad.
He-Man and the Masters of the Universe (1983) villain Skeletor, despite having a face that Standards & Practices must have had fits over, was thoroughly incompetent. He was so feeble at villainy, in fact, that the show resorted to two replacement villains: King Hiss of the Snake-Men, and Hordak, who suffered severe Villain Decay after his introduction. Neither were exactly scary themselves, but miles ahead of Skeletor.
Word of God is that the writers felt sorry for him, so they started writing stories where he'd team-up with He-Man against some outside threat, just so he could win occasionally and not look like a complete tool all the time.
Subverted in the 2000-era re-imagining. While Skeletor's still a Card-Carrying VillainSurrounded by Idiots, and Evil-Lyn is clearly his mental superior, Skeletor's clearly a threat this time around, having destroyed half of Eternia before the show starts, and twice defeating the Big Bad that the heroes themselves could not. While still sometimes played for laughs, and never shown as even 1/10 as threatening as Hordak, Skeletor crossed the line, at least.
Mister Smarty Smarts of Spliced, though there have been a few times that he has been a genuine threat to the other inhabitants of the Island.
Subverted in Mad Love where Batman actually admits that Harley Quinn was closer to killing him than the Joker ever was. Considering that this is the Joker, that says a lot!
The Ice King in Adventure Time certainly has the potential to be a great threat, being a powerful magic user but constantly thwarted by a boy and his dog doesn't do much for his reputation. His defeats are often so pathetic that they're depressing, and in the end, it's almost always Finn beating up an old man. He's so pathetic that one episode starts with Finn simply "grounding" him for misbehaving again (he tries to argue, but only gets more time added onto his punishment, ultimately he just gives in without even trying to actually fight).
To give an idea of his power, the Ice King once helped in destroying the world by causing it to freeze over after the nuke that created The Lich. Only his sheer idiocy and the fact he's verging on the border of a constant Heel-Face Turn because the heroes are his frenemies keeps him from being one of the show's biggest threats next to The Lich.
The fact that his crown drove him completely insane in addition to granting him his ice powers contributes a bit to his status as a Harmless Villain.
Adventure Time also lampshades it in "Conquest of Cuteness", where the villains are a race of tiny, cute creatures that can't do any harm at all. Finn and Jake feel sorry for them and pretend to be defeated.
In WordGirl, pretty much all of the villains qualify...but especially Chuck the Evil Sandwich Making Guy. I mean, just look at his name!
At least Chuck was always thiiiis close to possibly killing her, but, of course, not doing so. The Amazing Rope Guy, despite his name, can't even use the rope to his advantage. He even TIES HIMSELF UP when he was trying to get Wordgirl. That's just lame.
Plankton from Spongebob Squarepants. He has moments of competency, but even those don't go too well, mainly due to overconfidence or doing something so mundane, such as putting in a coin operated self-destruct mechanism, that his plans blow up in his face, figuratively and literally. This quip from Karen sums him up best:
"Plankton. One percent evil. Ninety-nine percent hot gas."
The E.V.I.L organization, which stands for "Every Villain Is Lemons", The extent of their villainy is shining flashlights into boats at Makeout Reefnote Good times, goooood times... and making fun of the young people.
The My Little Pony: Friendship Is Magic episode "Owl's Well That Ends Well" involves usually-good dragon cub Spike temporarily becoming an Ineffectual Sympathetic Villain. Spike is obviously stooping pretty low when he tries to make it look like Owlowiscious killed a mouse, but gets caught in the act way too quickly to do any major harm.
The diamond dogs of "A Dog and Pony Show" try to enslave Rarity to work in a gem mine. She has them wrapped around her hoof in minutes, and her friends' daring rescue was likely appreciated more by the diamond dogs than by herself.
Pretty much the entireRescue Rangers rogues gallery is quite harmless. And probably the whole reason that only a bunch of rodents are even bothered to take the time to deal with them. Case in point: inventing a self-propelled walking laser cannon capable of cutting up a glacier, (those things aren't exactly "just" a big ice cube) and only using it to warm up a giant vat of jello used to create an earthquake machine to break open a gold depository. Instead of, y'know, blasting your way in with said self-propelled walking laser cannon.
"Victor & Hugo - Bunglers in Crime" - despite being the alledged 'baddies' as their theme song suggests,they aren't exactly evil. The name of their 'No crime too small, no crime to big' company for hire is called 'Naughtiness International'. They never manage to pull off any crimes without mishap. On the rare ocassions they do, they always get arrested. Even stealing sweets from a sweet-shop was seen as a daring venture.
Arktos, the evil snowman, from Tabaluga. He is really silly and his evil antics always end in disaster. And during season 2, he even sells ice-cream to his enemies and spends half-his time whining about not being able to conquer Greenland.
Nobody really takes Dick Dastardly seriously because he's so ineffectual. He couldn't beat himself in solitaire even if he cheated.
The titular Invader Zim. If it isn't Dib who stops him, it's because of his own stupidity. Gaz lampshades it.