Lee Phillips of KateModern attempts to take revenge on Gavin and Tariq by...forcing them to play a treasure hunt game to retrieve their stolen software. He still manages to be a serious threat because there are other, decidedly less harmless villains who are also after the software.
Dr. Poque from Mega64 is arguably this, while he did kidnap and lock Rocko, Derek, and Sean in his basement, he's to much of a Butt-Monkey to be a real threat. Episode six of Version 2 amps this up to Woobie status.
During his first appearances in the Marik's Evil Council Videos, Dartz manages to be even more pathetic. Then, he suddenly becomes an Expy of Coiffio whose unfortunate accent causes both his henchmen and the audience to not be sure of whether his plans are the standard card game shenanigans or something much worse.
The evil AI Omega from Red vs. Blue can qualify for this, depending on who he's possessing at the time. In the body of Tex or any other sufficiently trained soldier, he's a genuinely terrifying threat. In the bodies of the Blood Gulch crew, and most especially Doc, he's little more than a nuisance.
The Goths at Superhero School Whateley Academy in the Whateley Universe. Despite serious attempts at summoning monsters and other evil acts, what they mainly manage to do is get their leader dumped into a Fate Worse Than Death and re-uniting Carmilla with her father (who is a monster). They also attack Phase... and get a Curb-Stomp Battle because they have no idea what they're facing.
Atop the Fourth Wall: Dr. Linksano starts out as this, especially since he was first used for a Breather Arc between the Mechakara and Lord Vyce storylines. He does show more competence later though, but mainly after his Heel–Face Turn to became a double agent for Linkara.
In a parody of the badly written villains of the comic, his Fourth Year Anniversary had Phelous (wearing a suit and mask) randomly come out of nowhere as his "mysterious" new enemy "Mysterior", who kept rambling about how he was mysterious and how Linkara had to solve the "Mystery". Both he, and a later replacement (exactly the same only with a different coloured mask and a slightly different name) were immediately shrugged off by Linkara.
Among the various horrors the SCP Foundation houses is SCP-1370, an artificial lifeform hostile to everything else. Luckily for everything else, 1370 is poorly designed to the point of losing a fight with a potted plant. Not even a paranormal potted plant, just a regular philodendron.
SCP-2006 is a potentially omnipotent shapeshifter, whose goal is to scare people for fun. Fortunately, the Foundation has it convinced that the most terrifying thing in the world are men in rubber suits from old 50s horror films (its favorite form is Ro-Man of Robot Monster fame). Because of that, it's almost completely harmless, and its scaring strategies consist of jumping out and saying "Boo!" Of course, if it were to ever realize how ineffective this is, it could quickly ascend to a Not-So-Harmless Villain.