Hwang Hwang in 2 Broke Girls, a gang leader who Han is deeply indebted to. He often comes off as a dork, for example he's shown singing "Call Me Maybe" in a karaoke bar and striking out with the waitresses; but he's still a professional criminal and not afraid to use violence to get what he wants. He threatens to cut off Han's toes if he doesn't pay his debts and keeps a man he mutilated in the corner of his hangout to prove he's not kidding.
Angel plays with this in regards to Daniel Holtz, a vampire hunter desiring revenge on Angel and Darla for destroying his life. Angel and Darla were always afraid of him but still didn't think of him as that much of a threat. When Holtz reappears in the present day, Angel and Darla realize just how dangerous he really is.
Tom Zarek and Gaeta in Battlestar Galactica. Tom spends most of the series as a placeholder for vice president or opposition, and Gaeta watching the radar. They eventually lead a coup against Adama and Roslin.
Carl Slater in Brassic. A seemingly inept police officer and Vinny's Sitcom Arch-Nemesis since school. In his first couple of appearances the gang easily outmanoeuvre and humiliate him, but by Season 3, he's been promoted to detective and is one half of the season's Big Bad Duumvirate. He manages to place an undercover in the gang, and build a case against them for their various crimes that could put them away for ten years. It only fails because the undercover tells Vin the truth at the last second, allowing them just enough time to destroy the evidence. Vin admits he wildly underestimated Slater, since he still thought of him as the snotty kid he used to pick on at school.
Warren and the other Nerds of Doom. At first, they're kind of silly with their arguments over Star Trek and the best actor to play James Bond, and their kinda weird attempts to challenge Buffy in ways that, really, were nothing compared to five seasons of big bads and various monsters of the week. Warren stops being funny when he tries to rape his ex via mind control and kills her when she tries to escape, and near the end of the season he shoots Buffy and murders Tara Maclay. Then one of the other nerds, Andrew, kills Jonathan, proving himself not just a source of comic relief.
The Mayor. At first, he seems like a self-serving politician tapping into supernatural powers for personal gain. Then it turns out he commands a small army of vampires and plans to become a pureblood demon. Oh, and he's also invulnerable; not just Nigh Invulnerable, invulnerable.
This becomes Spike's hat in Season 4. Buffy and company get used to thinking of him as harmless thanks to the chip implanted in his head that prevents him from physically attacking any humans, but he occasionally shows them that he could still cause them problems or even get them all killed, even if he can't attack them directly.
When Faith wakes up from her coma and plans to go on a rampage against the group, Giles and Xander run into Spike, and because he's lived with them, fought demons together with them a few times, and generally been unable to harm them, they make the mistake of assuming he'll be an ally. They ask him if he's heard anything about Faith, and Spike feigns concern, which makes them fill him in on the whole Faith situation (as Spike has never seen or heard of Faith before) complete with a physical description and the fact that she's looking for vengeance against the group. With this information in hand, Spike announces that he's going to find the rogue Slayer so he can tell her where they are so he can watch as Faith kills them. And thanks to their assumption that he's harmless, he even has a rough description of the person he should be looking for.
Spike: What do you need? Xander: Her. Dark hair, [raises a hand to about Faith's height] ye tall, name of Faith, criminally insane. Spike: Is this bird after you? Xander: In a bad way, yeah. Spike: Tell you what I'll do then: head out, find this girl, tell her exactly where all of you are, then watch as she kills you. [Spike smiles at Xander and Giles, then sighs in annoyance at their shocked expressions] Can anyone in your damn little Scooby club at least try to remember that I hate you all. Just 'cause I can't do the damage myself doesn't stop me from aiming a loose cannon your way.
Near the end of Season 4, he manipulates the existing tensions within Buffy's friends and successfully gets them to turn against one another.
When Harmony shows up in Season 5 with her own pack of vampires, the heroes can't take her seriously. Unfortunately, in the midst of taunting her, Dawn mistakenly invites her into her house, and we are reminded that while Harmony may be incompetent, she is still a vampire. Indeed, the minute she finds out that Harmony has minions, Buffy laughs her ass off but quickly changes her tune when she discovers that Dawn invited Harmony in, gathering a small arsenal of weapons and stakes. Then in season 8, she kills a Slayer with her own stake on national television and convinces the public that vampires are the good guys and Slayers are the bad guys, sending the US Military after them. All this from the seemingly brainless vampire that Buffy and Angel repeatedly refused to kill because they didn't see her as much of a threat.
At the start of the series, Chang's really more of a nuisance than a villain, and for most of the first three seasons, he's such a pathetic antagonist that one feels sorry for him despite his Jerkassery. Then at the end of Season 3, he gets Drunk with Power after being made a security guard and manages to take over the college after kidnapping the Dean, and afterward he nearly burns down the school with all the students still inside it.
Mr. Radd in "Regional Holiday Music" is introduced as an annoyingly cheerful, mildly creepy fellow who wants to get the study group to fill in for the Glee club. As with many of the show's plots, the joke is that Greendale is such a Cloud Cuckoo Land that students there would treat something so minor like a life-or-death situation. Then Mr. Radd lets slip that he murdered the original Glee club.
Vern, Psycho Loner and Big Bad Wannabe of Dark Oracle spent a season-and-a-half being treated as a joke by the main characters, who had far bigger problems to deal with in the form of their Evil Twins Blaze and Violet. Then in rapid succession Vern, finds and reads the comic book that shows Blaze and Violet's world, steals an amulet from Doyle and attempts to kill Doyle, Lance and Cally with it, absorbs some of the amulet's magic so that even after losing it he remains a threat, and frees previous Big BadOmen from the comic, eventually helping him trap Lance in the comic, and loosing Blaze in the process. Unfortunately for him, Blaze being on the loose means that Vern is again overshadowed, and ultimately has to pull a Heel–Face Turn when he realises Blaze is going to turn on him.
The Daleks are a meta-example. While they were always a threat and other characters rarely reacted with anything but terror, their numerous appearances over the original series' twenty-six year run heavily diluted any fear to be had from the motorised pepper pots. Thus the new series episode "Dalek" was written with the sole intention of showing a new generation that the Daleks were Not So Harmless, with a single imprisoned, crippled, powerless Dalek killing hundreds of people effortlessly.
On a lesser scale with the Daleks in First Doctor stories. In their third story "The Chase" they had the potential to become really dangerous when they acquire time travel and pursue the Doctor. However they come across as quite laughable here, one Dalek struggling over a simple math problem, falling over, and getting beaten by Funhouse robots. In their next appearances, "The Daleks' Master Plan" and its teaser episode "Mission to the Unknown" they came very close to conquering the Solar System and other Galaxies, and two companions die during the story.
In the classic series, there was The Master's appearance in "The Deadly Assassin". While never exactly harmless, his appearance here (after a lengthy hiatus) portrayed him less of a Friendly Enemy and more a ruthless Omnicidal Maniac, happy to tear the universe apart to save his own skin. In his next appearance, though his main plan is stopped, he ends up getting a new body by taking over a rather nice character. In the story after that, he goes on a killing spree and causes the Fourth Doctor's death.
This was the intention with the Cybermen in "Earthshock", after their poorly-received last appearance seven years earlier. The Cybermen come close to destroying the Earth and cause the death of one of the Doctor's companions, Adric, causing a case of Alas, Poor Scrappy.
Every time the Cybermen show up in a New Who finale, they are never the most dangerous threat. The Cybermen in "The Doctor Falls" on the other hand, take over the Big Bad role from The Master and get closer to killing the Doctor than any of the other recurring villains.
The Flash (2014): Season 3's first two episodes give us Edward Clariss, The Rival. He's a speedster obsessed with being the fastest... except he was not faster than Barry in the slightest. Furthermore, after seeing Barry defeat Zoom and his experiences with the Reverse-Flash, The Rival felt nothing more than a lackluster villain who lacked what made either of them personal with Barry. However, he ends up stabbing Flashpoint!Wally in the back and creates three tornadoes in an attempt to destroy Central City, thus reminding the viewer that no matter how unimpressive The Rival was compared to Reverse-Flash and Zoom, he is still a metahuman with dangerous powers that he intends to use to harm people.
Game of Thrones: Cersei Lannister. After about six seasons of being sidelined, outmaneuvered, and humiliated by the other players of the Game, Cersei snaps and has all of her rivals in King's Landing wiped out with wildfire before usurping the Iron Throne as Queen. She is directly responsible for killing as many or more major characters than anyone else has over all six seasons.
Recurring villain Junior Bunk is a minor player in the Mahoney crime family renowned for his cowardice, to the point of breaking down crying when he's arrested. He's also generally too meek and inept to command the fear Luther and Georgia Rae do, and absolutely no one on both sides of the law take him seriously. However, after going to prison, he hardens considerably and winds up shooting up the precinct, killing several police officers and near-fatally injuring several members of the main cast before being shot dead.
In "The Hat", Lewis and Kellerman are assigned to escort a fugitive back to Baltimore to trial. The fugitive is a cheerful, friendly Motor Mouth played by Lily Tomlin, well-known for playing lovable, comedic characters. She proves so charming that the detectives (and audience) forget she's been arrested for murder, resulting in her escaping and murdering another person before Lewis and Kellerman catch up to her.
When we first meet Sammy Tonin he's not taken seriously by anyone, he wears custom-made suits that are all the wrong size and is basically seen by everyone as nothing more than his father's messenger boy, but in "Ghosts", when his father is driven into hiding, he swiftly takes over the family business, turns his only rival's men against their boss and, after a moment considering whether to take Raylan at his word, has said rival riddled with bullets. The following season, he suffers a Villainous Breakdown and spends his time using chainsaws to torture people.
Dewey Crowe is the show's resident Butt-Monkey and gets no respect from the other criminals or law enforcement. However, season 3 reveals that when desperate he can be extremely violent and dangerous though still incredibly dumb. In season 5 he murders a man.
Dickie Bennett is Smug Snake par excellence who is probably the least threatening of the Bennett crime family both physically and mentally. However, he's shown time and time again he's a vicious little scumbag and that if you turn your back on him, be prepared for him to shoot you dead without remorse. Just ask Raylan's mom Helen.
Kamen Rider Kuuga: Subverted with Xu-Goma-Gu, the Bat Grongi. In his first appearance he's a Starter Villain and barely stronger than a regular human. When he comes back later in the show, he's used a discarded piece of Big Bad N-Daguva-Zeba's body to evolve himself, and eventually evolves to be so powerful that he easily defeats Kuuga. With his new power, he goes to challenge Daguva...who then kills Xu-Goma-Gu in mere seconds, demonstrating that he was never even close to being a real threat.
Kamen Rider Double: Wakana Sonozaki is by far the least powerful member of her family, all of whom possess unique and extraordinarily powerful Gaia Memories with a plethora of abilities. Aside from an arm cannon, Wakana's Claydoll Memory only gives her a Healing Factor, and it's one that involves shattering into pieces from even minor damage before reconstituting herself; she's so weak in fact that another member of the family shows off his ability to beat her in a fight without even using his own Memory. Once she unlocks Clay Doll's potential as a cleric of the Akashic Records, however, Wakana becomes so powerful that the only time the heroes even try to fight her, it lasts barely a minute and they don't land a single hit on her. By the end of the show, she's only beaten by Talking the Monster to Death, and it's not even Double who does it.
Kamen Rider OOO: Dr. Maki starts out as a creepy emotionless scientist with a Morally Ambiguous Doctorate and a weird fixation on the Creepy Doll he carries around on his arm. While genuinely unsettling at first, the way he flips out whenever he loses his doll gradually turns him into a joke. He's only dangerous in that he's allied with Kazari, the strongest and most cunning Greeed, and meeting one of the main characters who looks like his sister appears to set Maki on the path for a Heel–Face Turn. Then he fully recovers the memories surrounding his sister's death: he killed her, in a fit of jealousy, and looking back on the event, he decides he was right to do so. Cue him obtaining the Purple Core Medals, transforming into a Greeed himself, hijacking Big Bad status from Kazari (directly killing him in the process), and coming within inches of destroying the planet. Right before his final showdown with OOO, Maki throws the doll away himself, demonstrating that any comedic elements he once had are now gone.
LazyTown: "Records Day" has an unusually malicious moment for Robbie, where in an attempt to get the World's Laziest Person world record he resorts to attempting to murder Sportacus via a soccer ball catapult.
Percy, the Big Bad of Nikita, started out seemingly ineffectual, always being Out-Gambitted by Nikita at every turn. However, as the series goes on, he becomes worse and worse.
One episode of NUMB3RS has a pair of polite bank robbers. They walk in, request the money, say thank you, and walk out. They are even polite enough to hold doors open for people. Really harmless robbers with a cutesy nickname, or so people think until Charlie predicted their target and Don and a team tries to arrest them. That is when they demonstrated that not having needed to call for backup is not the same as not having backup, and not having needed to use violence is not the same as being unwilling to use violence. Turns out they are ex-special forces working to a deeper plan and perfectly happy to use assault rifles, car bombs, and expertly knife a janitor that gets in the way — just hadn't needed to before.
Power Rangers Lost Galaxy: Becoming Not So Harmless was what Trakeena's whole character is about. At first, she's Big Bad Scorpius' spoiled daughter and spends most of the time whining or backstabbing the villains who do know what they're doing in order to rise in the ranks. Eventually, she leaves, eventually meets up with an old ally of her dad, and gets some combat training. The real fun begins when The Starscream, Deviot, arranges Scorpius' death and succeeds. Trakeena returns to take his place... and the new, badder Trakeena is worse than her dad ever was. She starts out as a competent and more proactive Big Bad and gets more and more driven (and insane) until finally reaching unimaginable heights of evil.
Power Rangers Ninja Storm: In Lothor's very first appearance, and during a time-travel journey back to his days as a man, he was formidable, but he seemed very bumbling/ineffective throughout the season, lamenting how his plots always failed and his soldiers were being destroyed...until the finale, where he revealed that he was filling up the Abyss of Evil with dead soldiers in order to cause all hell to break loose on Earth. To this end, he willingly employed a backstabber and allowed himself to be destroyed to lead the charge of bad guys. He never actually loses in a real fight against the Rangers and has to be sealed away in the Abyss. And when he returns for the crossover with Power Rangers: Dino Thunder, he escapes the Abyss of Evil, captures Sensei, and tricks the Wind Rangers into using corrupted power coins which brainwash them. He then proceeds to take them and two monsters from the Abyss with him to attack the ninja school and capture the students again.
Stargate SG-1's Lucian Alliance gained a reputation as being a bumbling band of smugglers whose M.O. roughly came down to spreading evil space corn throughout the galaxy. When they make their reappearance in Stargate Universe, they do so replacing the goofball routine with a new "ruthless band of badasses" one. In the pilot, they have several Ha'taks give trouble to the General Hammond, a Daedalus-class battlecruiser upgraded with Asgard technology (including those plasma beams that can slice through Ori shields like they're made of paper). The Ha'taks themselves were for a number of seasons considered nothing more than a joke. And why not? The Lucian Alliance are not the Goa'uld, they're human (most of them) and have as much ingenuity as Earth-bound humans.
In Star Trek: Deep Space Nine, in "Changing Face of Evil", the Dominion allies with the Breen, a race that can only live in the cold, and was previously known only as pirates and slavers, and are best known among fans for wearing a copy of Princess Leia's bounty hunter disguise from Return of the Jedi, so the first reaction was "WTF? Is the Dominion going to make an alliance with the Kazon next?". Then the Breen attack Earth and then they whip out the energy draining gun, defeating 300 ships at once and endangering all others.
Mirror Hoshi on Star Trek: Enterprise. At the start of the two-part episode, she is the captain's sex-bunny and background character in all the plotting and conspiring; as it ends, she has just made herself Empress.
The Borg in season 3 of Star Trek: Picard. While never harmless, their reputation as an unstoppable force has been really brought down by Star Trek: Voyager. And now the Queen nearly lays waste to Earth just as Starfleet is celebrating its latest triumph.
Marlo Stanfield's first appearance in The Wire is very unassuming (blink and you'll miss it). Furthermore, the Barksdales and everyone else initially dismisses him as just a small-time dealer of no consequence. Fast forward a year and many row houses later...
The Count from Young Dracula is often made fun of in-universe and generally regarded as a washed-up has-been among the vampire community. Every now and then, however, he'll make reference to the fact that in his heyday, he was Vlad the Impaler, killer of thousands and one of the most horrifically ruthless dictators ever to walk the face of the earth. The one time he is cornered by a dangerous enemy and it is made clear he will not be able to weasel out of a fight the audience sees a swell of his real power followed by the Count making a necklace from his opponent's extracted fangs after the Fight Unscene.
