Spider-Man has his share, though given that he's got the largest Rogues Gallery in Marvel, you'd expect as much. From the 80s British punk and punctuation-themed Typeface to the even more pathetic Grammar Nazi Spellcheck to ditzy Playboy Bunny the White Rabbit, who's so stupid that she had to hire actors to pretend to work for her, because nobody would for real note Not even the Big Wheel returns her calls. The Walrus is also pretty notable here: Spider-Man actually almost got his ass kicked by him because he couldn't stop laughing.
The Walrus is a subversion actually. He's a deadly killer, but his costume and MO is so lame that people constantly think he's this. So he's more a Not-So-Harmless Villain.
The Spot is another subversion; the character was treated as a complete joke (to the point that Spider-Man laughed at him in his very first appearance) until the writers remembered that having portals all over your body and being able to make portals is actually a really awesome power. Since he couldn't realistically work as a joke villain, they went the other direction and now Spot is depicted as being a potentially deadly villain who simply doesn't know how to use his full potential. Most adaptations have followed that example.
The above-mentioned Big Wheel actually acknowledges that he's not cut out for supervillainy. He disappeared for several years and when he turned up again, it turned out that he'd quit because he knew he was completely outclassed. The animated series however depicted him as much more competent.
The Stilt Man. The Leap Frog. In the early days of his comic, Daredevil was the MST3K of comic book super heroes.
Bafflerog Rumplewhisker of "The Wizard's Tale" is the latest in a long line of really unpleasant people serving the forces of evil that keep their world in a state of permanent twilight (because they haven't yet found the MacGuffin to make it permanent night). Unfortunately, Bafflerog's spells tend to be much less evil than he intends, such as trying to call up a huge storm and getting a pleasant rain that breaks the drought on the town, summoning a hail of locusts and getting a shower of roast chickens instead, and making friends with the creature he's supposed to be torturing for the location of the MacGuffin. He also phrases his spells in the form of limericks.
Killer Moth is essentially the Butt Monkey of Batman's Rogues Gallery. He's considered the weakest supervillain in Gotham and is usually captured pretty easily by Batman and company. Eventually he got tired of being picked on all the time and not taken seriously, so he made a Deal With Neron and became Charaxes, a deadly cannibalistic moth creature that spits acid. However, nobody really liked this change and so Moth pretty quickly got retconned back to being the loser we all know and love.
Also The Riddler...sometimes. Nowadays, the Riddler is often portrayed as a fiendishly clever yet endearingly incompetent villain.
Unlike some, he actually stresses out over this, frustrated with how he is compelled to give Batman clues due to his neuroses — and is kept from revealing Batman's secret identity (which he managed to puzzle out) by the fact that a riddle everyone knows the answer to isn't a very good riddle at all.
In another arc the Riddler, due to a year long coma, had lost his compulsion, and goes into business for himself as an extremely successful (if not always correct) private detective.
The Joker occasionally plays with this, likely for his own amusement. On any given day, you don't know if the Joker that Batman is facing is a sadistic Monster Clown who'll hold the city ransom and threaten to burn down the whole place, or a loony who concocts an elaborate (*ahem*) Batman Gambit just to hit Batman in the face with a pie.
Like everything else about him, this just adds to the Joker's disturbing qualities. He's the only villain listed in every villain trope page who could GENUINELY be all those at once. He's just that friggin' bonkers. Deadpool comes close to being Marvel's answer, however. If you read some of Deadpool's best fights, while turning to THAT IMAGE of him WEARING JEAN GREY'S OLD COSTUME, you readily see it.
And then there's Calendar Man, a guy with a bunch of ridiculous costumes and no powers who performs crime sprees related to dates. Despite an attempt to turn him into a Hannibal Lecter-esque figure in The Long Halloween (which later influenced his really creepy appearance in Batman: Arkham City), he never accomplished anything other than showing up at the top positions of many "Worst Batman villains" lists. Most mentions of his name are nothing more than cheap punchlines. Meanwhile, the Holiday killer used a similar modus operandi and became one of the most feared and impacting figures of the criminal underworld.
In the Knightfall arc, Bane breaks all the supervillains out of jail simultaneously, and Batman is so exhausted by the effort of recapturing them all that even fourth-rate villains start becoming a serious threat. The one exception? Maxie Zeus, who escaped still wearing his straightjacket and runs himself face first into a tree.
One of the villains mentioned in Watchmen is "Captain Carnage", who pretended to be a super-villain because he got pleasure from being beaten up. This backfires badly when he tries it with Rorschach...who dropped him down an elevator shaft.
Marvel's alternate-universe Squadron Supreme has Pinball, a guy whose power consisted of inflating his green jumpsuit into a ball and rolling into people.
Back in the 80's, The Avengers had occasional skirmishes with Fabian Stankowicz, AKA The Mechano-Marauder, a lottery winner turned power-suit-wearing supervillain. From the very beginning, the Avengers never took him seriously: in his first assault, Iron Man considered him so low a threat that he turned down several offers of assistance from the other Avengers. However, Fabian's definitive low point was when he attacked them during a taping of Late Night With David Letterman and briefly managed to gain the upper hand...only to be knocked out by Letterman himself.◊ Eventually, Captain America offered him a spot on the Avengers support crew, mostly to keep him from endangering himself further.
Explored seriously with Jarvis Poker the British Joker, in Paul Cornell's Batman spin-off Knight & Squire. Jarvis takes on the appearance of the original Joker as a tribute, but always stays the harmless prankster that the Joker has been portrayed as in the franchise's most Lighter and Softer versions. It's even implied that he may primarily act as a trickster mocking and stealing from evil rich people. Things get very sad when, first, he gets terminal cancer, and then the real Joker comes to Britain and decides to show Jarvis what a genuine villain acts like, forcing him to die in a Heroic Sacrifice.
Zipi y Zape: Manitas de Uranio, resident burglar of the neighborhood, is totally inept and gets owned by the twins every time he tries to steal from their house.
The majority of Romans in Astérix stories, especially as the reputation of the invincible Gauls spreads and they start running from any hint of conflict. Most of the generals of the fortified camps surrounding the village are this combined with Punchclock Villain and tend to act out of fear for what the higher-ups would do if they were not seen to be acting, and the foot soldiers tend to be put-upon Mauve Shirts who would rather be doing anything else.
Superman villain the Prankster is a perfect example of this. His schemes usually only amount to pranks and gags to tick Superman off. Thing is, Prankster is well aware that he's harmless and he doesn't want to be a threat. See, Prankster makes the money for his fancy toys and tricks as a "distraction for hire" of sorts; essentially, other supervillains in Metropolis pay him to launch some wacky plan just big enough to draw Superman's attention and while the Man of Steel is busy dealing with that and pounding Prankster's head in, the employers are in another part of the city pulling off their actual crime. Thus Prankster gets money and an opportunity to screw with Superman, while the employers get to make off with their loot without worrying about a big flying alien hurling them across the city. Everybody wins.