Harley was often treated as genuinely misguided, so the audience sometimes forgave her for her more violent behavior depending on how softening a particular episode was.
In the comic-turned-episode "Mad Love", Harley did manage to succeed in trapping Batman. Batman's only hope was to have her inform The Joker, who he knew would free Batman because it wasn't HIM that defeated Batman! Batman even admitted that Harley came closer to killing him than the Joker ever did. Harley also suggested just shooting Batman, instead of elaborate death traps. Ironically, at the end of the episode, Harley almost succeeded in killing Bats with an elaborate death trap, while the Joker, who previously slapped Harley for even suggesting such a thing, tried simply shooting him...and failed.
"The Man Who Killed Batman" was focused around Sidney Debris AKA "Sid the Squid", a nebbish and meek bumbling mob underling who dreams of being a bigshot. He gets his wish when Batman is apparently killed and his gang believes Sidney did it. Unfortunately, as Sid finds out, that reputation comes with a price... The episode has a happy ending for Sid, however. He still goes to jail, but Batman lets everyone keep believing that he almost killed Batman and made a fool out of the Joker, turning Sid into a celebrity in prison.
ALL of the "villains" from "Make 'em Laugh", though they're only villains because they were brainwashed by The Joker. They're all pretty ineffective, but most notably is the "Condiment King". Even Batman takes pity on the guy.
Police Radio: Suspect is a male costumed extremist armed with what appears to be a... ketchup gun.
In one of the early World Premiere Toon shorts, the Girls actually commit a bank robbery solely to show the Boys how it's done. When the Girls are brought in for the crime, the boys turn themselves in, in an attempt to appear "big time".
In another, during the actual series, the Boys stumble upon Mojo Jojo's Deathtrap plans, and they, along with the Girls, mistake it for a "scavenger hunt" — so they find all the things it calls for and put it together, and once it's assembled, the Girls think it's a theme-park ride, so they willingly submit to the plan intended to destroy them.
In another episode, the Boys catch a cold while loitering on the grass in yet another attempt at crime. Even though they end up unwittingly mutating the cold into a deadly strain of virus and even more unwittingly starting an epidemic in Townsville, the viewers still can't help but feel sorry for them.
And in another episode, they manage to actually succeed at stealing an orange, for once, and when it splits apart, are reminded that, as amoebae, they are capable of multiplying. There is quickly an army of them, and the only thing they can think to do is to steal all the oranges in Townsville (although this does cause the citizens to contract scurvy).
The Toilenator from Codename: Kids Next Door badly wants to be a villain, but is far too wimpy and incompetent to pull it off. He's a minor inconvenience to the KND, and most of the bad guys try not to be seen with him because of his clingy Bumbling Sidekick personality.
He's a Not-So-Harmless Villain though, as he's able of using his "toilet powers" to "flush" the entire Grand Canyon with milk.
He also managed to defeat the five main characters by himself on one occasion after getting fed up with being treated like garbage. Only not really. He beat the entire team of villains on his own, mistaking them for the kids.
Odlaw in the animated series Where's Waldo? (Where's Wally?). As so many bad things keep happening to him in the name of comedy, and all he ever wants is to commit a single act of theft, you have to feel for the guy. Also, his determination is admirable!
Killgore from My Life as a Teenage Robot is an odd example, in that he's inneffectual BECAUSE he's so sympathetic. People are finding him too cute (being that he is a wind-up toy) to see him as a threat, including his self-declared nemesis Jenny. However, he also proves to be a Not-So-Harmless Villain, as he's quite capable of going to extreme lengths, such as somehow managing to rebuild the deadly Armageddroid, to prove he's dangerous.
This is reinforced by Jack being probably the only fictional character, let alone villain, to have a breakdown failing to interrogate a parrot that simply repeated everything he said.
The problem is that Jack is 'trying' to be a villain yet is fairly bad at it. When he turned to good for a while before returning to evil, it wasn't that he was planning to betray them from the start, he 'did' try to be good but was afraid he would fail at being good just like he failed at being evil.
Most of them are of the Not-So-Harmless Villain type. It's shown that the reason OSI and such tolerate the supervillains' stupid games is that it keeps them from committing real crimes or blowing up cities. (Those who don't play the game have to deal with SPHINX.) The Monarch, in particular, is a special case. When he was taken off of Dr. Venture, he was unhappy with the normal game and proceeded to kill 5 heroes in a short time.
Doctor Mrs. The Monarch is the most competent villain and, quite possibly, the most competent character on the entire show. Even the Sovereign of the Guild respects her.
Doctor Killinger's entire reason to exist seems to be to snap out villains from this trope and into Not-So-Harmless Villain instead.
Doctor Killinger's fourth episode, The Doctor is Sin, makes a pretty persuasive argument that Rusty Venture himself is this. Killinger spends much of the episode giving Venture Industries "efficiency" training, with the true aim of turning Doctor Venture into a real, Guild-bonded supervilain.
Wile E. Coyote. In fact, one of the laws of the Road Runner cartoons is "The audience's sympathy must remain with the Coyote."
Sylvester the Cat was usually depicted as one of these.
It's very difficult to hate the likes of Marvin the Martian and Elmer Fudd.
Yosemite Sam was actually a deliberate subversion of the trope, because audiences were starting to favor Elmer too much. The idea was to feel sorry for the guy, but it was getting to the point where Bugs was starting to look like a relentless bully instead of a wiseacre outwitting the buffoon who was trying to victimize him. Sam was both smarter and more belligerent than Elmer, meaning that Bugs was free to lead him on all he wanted. But even Yosemite Sam, while pretty dark for a Looney Tunes villain, was still fairly ineffectual compared to the average non-Looney-Tunes villain.
Ditto for Sky-Byte and his Team Rocket in Transformers: Robots In Disguise. Except that Sky-Byte would actually be leadership material if only a few things were different. It's just that he lacked the only two qualities that really mattered for a leader: aptitude and intelligence.
He has a few positive experiences even in the first season, and got so much screen time not directly related to suffering or fighting the Gaang that he was practically a main character all along. He was even allowed to win against the other villain and get his first CMOA.
Frisky Dingo's Killface is a pseudo-cultured, incompetent supervillain whose plans are often derailed by trivial matters and lacks knowledge of common subjects (it's a revelation to him that P.C. stands for "personal computer"). He's still more likable than "hero" Xander Crews, though.
Killface is so sympathetic, especially when compared to Jerk AssDesignated Hero Xander Crews, that it's easy to forget that he brutally killed two people in the pilot and has added to his body count throughout the series. It helps that some of the other members of the cast have committed similar misdeeds and/or are Asshole Victims.
Invader Zim qualifies for this trope most of the time; more often than not, his schemes are thwarted by the Ditz portion of his Genius Ditz personality, rather than by his arch-nemesis or his Cloud Cuckoo Lander robot. Of particular note is the episode where he survives a Training from Hell in order to receive some Humongous Mechas from his leaders, only to be shot into a sun for his troubles.
Carl anyone? The commercials for the next episode suggest he'll join the heroes so he can keep up with everyone else.
Dr. Drakken from Kim Possible never gets the respect he thinks he should have; he always fails his capers, sometimes even without the help of Team Possible. He often gets mistaken for the more respected Dementor and, at the end of the series, he is outright told how much of a failure of a villain he has been (despite having come closer to taking over the world than any of his peers, and ending up with much of the credit for saving the world from the Alien Invasion). If it wasn't for his Dragon, Shego, he wouldn't be a villain at all.
Arguably, every villain in Kim Possible is like this, aside from Shego, who's the only one with any amount of competence or fighting ability.
Keeping Shego on HIS payroll should be considered extremely competent, especially when there are villains like Senor Senior Senior, who has Scrooge McDuck levels of moolah.
Cobra Commander, who was constantly mocked, ignored, or pushed aside not only by other would-be world conquerors, but by his own minions.
Of course, he was never anything but effective and unsympathetic in the comics, where, among other things, he killed his own son. Oh, and he used to be a used car salesman, thefiend!
He does get the ineffectual part still - sometimes as part of a plan, sometimes because it's an imposter performing poorly. And sometimes, Destro just plain doesn't like him, and is willing to take the loss just to make him look bad, mostly because of his 'thing' for the Baroness.
The miniseries G.I. Joe: Resolute is also a subversion. Cobra Commander actually has a speech where he claims his previous incompetence was just an attempt to force his minions to think outside the box. He wipes Moscow from the face of the Earth just to prove that he could, and by the end of the series, he's so unhinged that he's hacking his own men apart with a sabre. His plan still failed, of course, but holy shit was he badass.
Of course, after his Arrogant Kung-Fu Guy resume is firmly established and he has shamelessly brutalized the entire rest of the cast, others see this as simple Kharmic retribution. Pride goeth before the fall, after all, and a Humiliation Conga was really no less than Tai Lung deserved at that point.
Until they start gunning down unarmed pacifist, cracking open escape pods so the helpless people on board will die in space, and Zerg Rushing that is.
Plankton from Sponge Bob Square Pants. After a while, you just start to feel sorry for the guy, especially when compared to how heinous Mr. Krabs' actions to get more money have become. It's more prominent in the post-movie episodes, where he could easily be one of the Trix Rabbit's drinking buddies. Granted, he gets a Not-So-Harmless Villain moment in the movie, but still...
Most of the time, it seems that he just wants some manner of success. In the cruel Yank the Dog's Chain episode "Plankton's Regular", after getting just one regular customer, he immediately stops trying to steal the Krabby Patty secret formula. Mr Krabs and Spongebob still found it neccessary to "thwart" him.
Of the primary villains of the earlier series, No-Heart and his niece Shreeky don't count. No-Heart was a legitimately powerful and evil sorcerer who had a habit of blasting Beastly with lightning bolts whenever he screwed up; and while Shreeky never actually did anything evil, she was a Spoiled Brat with a voice so loud that she made No-Heart wince. Mr. Beastly, No-Heart's primary lacky, definately fits somewhere between here and Butt Monkey. In the one episode that Beastly had, with him in the spotlight, him infuriates No-Heart by breaking No-Heart's crystal amulet (which is the source of his shapechanging spells), then breaks No-Heart's throne (something he knows No-Heart will be livid about), get turned into a horrific mishmash of animals while using No-Heart's broken amulet to catch some of the Care Bears, then be blackmailed into letting the Care Bears go after they tape-record him chanting a litany of "I care" to break the broken spell and be turned back to normal, and then, when No-Heart arrives, having calmed down due to finding an even more powerful crystal, he sits on his crudely repaired throne...and it breaks to pieces. Meaning more electroshocking for Beastly.
The Box Ghost of Danny Phantom draws the line between this and Harmless Villain. He has the potential to be a great baddie (if one episode and his badass future self is any indications), but he just never makes it. Out of all the ghosts Danny has fought, Box Ghost is strictly in the "Who Cares" category, but he tries, he oh so tries.
Voltar and the League of Super Evil. Guy is just so very motivated and happy about every plan or scheme he thinks up, no matter how trivial, that you just have to root for him. I mean, how many villains are ecstatic about throwing an 'EVIL' barbeque and not inviting their uncaring neighbors?
One of the episodes involves a highly convoluted plot by the League...to make the pizza delivery boy late so that their food will be free!
Nope, he was still going to retain this role. In one interview with screen-writer Ben Hurst regarding the third season that never arrived, it was revealed that Snively was going to take a shot at becoming the new Big Bad, only to be shortly upstaged by Ixis Naugus, and would later make a Heel-Face Turn and join the Freedom Fighters.
Dr. Ivo Robotnik and his henchmen from Adventures of Sonic the Hedgehog. While Robotnik often tries to do something rrrroten, he ALWAYS fails horribly, and Sonic torments the doctor so sadistically, that it becomes hard to sympathize with the heroes.
Even more so are his minions, Scratch and Grounder. While Robotnik could at least genuinely cook up a malicious plan every now and then, his duncebot's Wile E Coyote-esque traps hardly ever worked on anyone but themselves.
Dr. Heinz Doofenshmirtz is a self-proclaimed evil scientist whose endless string of [something]-inators are perpetual failures. He also had a ridiculously terrible childhood, never wins any of his battles, seldom gains any lasting happiness, and once lost a fight with a potted plant. The only thing saving him from complete Woobiefication is that he's always back the next episode, enthusiastically hatching yet another evil scheme.
On the other hand, his alternate-universe counterpart, with just onemorehumiliation during the Trauma Conga Line that was his childhood, was a genuine threat and not sympathetic at all.
Sandman in The Spectacular Spider-Man can never quite get his big score. Before his superpowers, Spider-man jokes about how many times he's been caught. After, he can actually fight Spidey, but then proceeds to forget or be unable to keep his take when he escapes down the drain. He also gets a couple of Pet the Dog moments when it's revealed that while he cares a lot about the Big Score, he doesn't really want to hurt anybody (other than Spider-man, of course).
The Lobe, archnemesis of the titular character in Freakazoid!. Despite being fiendishly brainy (quite literally - pretty much his entire head is made up of brain), he's extremely sensitive and insecure, and Freakazoid was once able to defeat him with nothing more than some harsh verbal criticism of his scheme.
Dr. Reginald Bushroot of Darkwing Duck. He mutated himself in an attempt to impress a girl. When that went about as well as expected, most of schemes throughout the series involved trying to grow a companion or feed his plants. He certainly seemed like a nice enough guy most of the time, only turning violent when Darkwing tried to stop his plans.
Hack and Slash, the bumbling minions of Megabyte, in ReBoot. In fact, they are justified in being bad guys by the fact that the heroes always stop them before they could do anything really awful. When the heroes fail to arrive to stop them from killing a traitor to Megabyte, they let him go off on their own and undergo a Heel-Face Turn.
Skeletor in He-Man and the Masters of the Universe (1983) was so ineffective that the writers felt sorry for him. One stated in an interview that part of the reason they wrote a few Enemy Mine episodes was that it was the only way they were allowed to have Skeletor come out ahead for once.
His 2002 incarnation, on the other hand, was every bit as powerful, terrifying, and evil as he claimed to be.
Control Freak from Teen Titans. Despite being able to animate the inanimate to do his bidding and inadvertantly altering television frequencies to literally rot people's brains, he STILL didn't get on the Titans' list of main villains.
Control Freak:The Puppet King?! They fought him ONCE!!
Lucius Heinous VII on Jimmy Two-Shoes. Despite literally ruling Miseryville, the main characters either don't fear him or don't respect him. He desperately tries to be the Big Bad, but fails horribly.
Tom, from Tom and Jerry, was so ineffectual and sympathetic that, in many cartoons, one failed to see how Jerry was even a victim. Particularly egregious examples, in fact, would cite that he wanted nothing more than to leave Jerry in peace, and Jerry could not stop antagonizing him and trying to ruin his life. Often, the shows started with Jerry trying to steal Tom's milk, break into a safe/refrigerator/ship that Tom was guarding or just being a dick in general. Granted, sometimes Tom's methods can get a bit extreme, he's just trying to protect his property or doing his job.
Toad and the rest of the Brotherhood, at least by Season two. At first, they were at least even with the X-Men, and were able to over power them in one episode, except for Toad. But slowly, each one got more and more Pathetic. Pietro became more cowardly, Blob became more dumb, and Avalanche went through massive character Derailment. In season 3, they were bested by only Two X-Men, one being the weakest member. It was why the Acolytes were introduced, who were definately not this.
Usual, given that this is the reason why they're so popular, with people playing up the ineffectual sympathetic part, and ignoring the vilain part.
Of course this all gets flipped on it's head once we learn his Backstory Horror. At that point, not only is the sympathetic part taken to whole new levels, but the protagonists start treating him better and he develops into the Token Evil Teammate.
The Cute King and his subjects are trying so hard to be threatening in spite of their inability to charge down a hill without literally coming apart. Finn and Jake take pity on them, on the basis that they'll either win or die, and they're not going to win, and convince a bunch of people to let themselves be "killed", using ketchup to fake the wounds.
Ben 10: Alien Force: though he does becomes a threat on occasions (he was actually dangerous in his first two appearances), Albedo was this from the beginning and becomes more so as the story goes on. He is doomed to be trapped in a human body he despises, and all he wants is getting his original form back. As a matter of fact, when he finally gets his form back in one episode, he makes it clear he has no more reason to fight Ben, and prepares to leave Earth... only to immediately revert to human form.
Leonard McLeish from The Hub's Pound Puppies series. He's self-centered, short-tempered, and clearly more concerned with impressing people and getting promoted than actually doing his job as head dog catcher, but he's not really a bad guy.
Killer Moth from The Batman is given this treatment when he joins "Team Penguin". All he's ever shown doing is using a cocoon gun that continuously backfires on him and make coffee for the Penguin. This changes however, when some chemicals change him into a giant moth mutant.
Bull Gator and Axl in Taz-Mania. In the very meta episode "Retakes Not Included", Bull even observes that they are what passes for villains on the show.
The My Little Pony: Friendship Is Magic episode "Owl's Well That Ends Well" involves the usually-good dragon cub Spike temporarily becoming a villain, but definitely of the "ineffectual sympathetic" variety, with the emphasis on "sympathetic". For context, when an owl named Owlowicious shows up to do some of the work Spike had been typically doing for the girls, Spike ends up getting less attention from them than before, and in turn, resents the owl a fair bit. After being scolded by Twilight for lying about a book not being there, he thinks the owl set him up, and in turn, tries to do the same to the owl, by planting a fake dead mouse with ketchup blood in Twilight Sparkle's room; he gets caught in the act. After running away, ending up encountering a dragon while gone, and then being saved from the dragon by Twilight and the owl, he apologized for the way he was behaving and is back to being one of the good guys.
Except in the episode "Secrets of My Excess", however this time, Spike is transformed into a gargantuan rampaging beast that almost completely demolishes Ponyville. Even then he may lean into this since it's all for the sake of hoarding "gifts".
Most of the Rogues Gallery for the show act as this or mere petty bullies. The foes used in the two part specials are the only notable exceptions, and even then their detrimental arrogance and the often humiliating manner they are taken out almost makes you pity them.
Gargamel in The Smurfs (and pretty much most Smurfs villains except Balthazar).