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.
Though a special prize has to go to Spidey villain the Spot, until he got a revamp to make him a major threat. During his first appearances, he was so pathetic that Spidey couldn't even be bothered to fight him, and instead, he falls over laughing at the mere sight of him. He actually turned up in Spider-Man: The Animated Series and kicked seven shades out of Spider-Man.
Daredevil arguably has it worse. The Matador (not to be confused with the otherguy)? His entire gimmick is about obscuring your vision with his cape, which, for Daredevil, doesn't do anything. Stilt-Man? Exactly what he sounds like. The Gladiator? Just a musclehead with anger management issues who happened to have a costume lying around. Daredevil basically has three legitimately threatening villains (one of them transplanted from Spider-Man's rogues gallery), and about 30 or so total losers.
The Stilt Man. The Leap Frog. In the early days of his comic, Daredevil was the MST3K of comic book super heroes.
The Gladiator got turned into a Not-So-Harmless Villain when they started playing his early ramblings and characterization, which by more modern and mature standards sound silly and slightly delusional, very seriously and turned him into a violently unbalanced crazy person with an unhealthy love of buzz saws and ancient Roman culture.
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 started out as a pathetic bank robber who got apprehended very easily and eventually got tired of being picked on all the time and not being taken seriously. He made a Deal with the Devil and became Charaxes, a deadly cannibalistic moth creature that spits acid.
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.
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.
Jarvis Poker, the British Joker in Knight & Squire, is a Harmless Villain to the extent that he doesn't really qualify as a villain. He appreciates and duplicates his American counterpart's sense of style, but finds actually committing crimes to be terribly gauche. However, the Knight does have genuine (if silly-seeming) villains to deal with, such as Morris Major and his Nazi Morris Dancers, and the Bad Kings of England.
Zodon from PS238. He is an Evil Genius, and is both intelligent and competent...But he's also seven years old, too cynical to ever be truly malicious (possibly because comparatively victimless crimes like insider trading and 'tampering in god's domain' means less detention time), and most importantly, is the comic's Chew Toy. Almost everything he tries his hand at will, at one point or another, fail horribly. Ironically, Zodon has proven himself much better at aiding the 'good' children (usually unwillingly or very reluctantly), and also saved the world against an Alien Invasion at one point.
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.