The Bill featured a guy playing an "Assassins" style game using a realistic looking paint gun in public. People who play these sort of games do not use realistic weapons. One guy from the Oxford University Assassin's Guild did that and encountered some armed police.
The 'armed police' problem also happened with Glasgow's Assassin's Guild.
There was also the "Down the Rabbit Hole" episode which dealt with Second Life. This spanned over two episodes rather than the usual one.
And one about "vampire cults" who drink each others' blood. Surprisingly, no vampires committed the crimes. The episode treated vampirism like an unpopular but venerable religion.
Yet another episode involved the owners of adult dolls (although it turned out that the doll ownership was irrelevant to the murder). Basically, CSI: New York, like all of the shows in the CSI Verse, is pretty much in love with this trope.
The famous episode "Fur and Loathing", set at a furry convention began it all. The portrayal of furries caused considerable controversy in that fandom. The episode was even a Jump the Shark moment for some, who saw it as the start of a freak-a-week format.
An episode where the victim, a powerful casino owner, was an adult baby in his spare time.
"Slaves of Las Vegas" introduced viewers to Lady Heather and her BDSM club. Lady Heather actually became a well developed (if only sporadically recurring) character.
A murder-at-the-Star-Trek-convention storyline, albeit with the serial numbers filed off. Trekkies, Trekkies everywhere...
The CSI: Miami episode dealing with videogames, in which the characters had to actually play the game in question to find out its plot, which was necessary for them to solve the cause. Why they don't just look up its plot online is anyone's guess. There's also a notable level of New Media Are Evil in the episode. In the episode, a video games company decides that a good advertising tactic for their GTA clone (which somehow still had "levels" and "points") is to give teenagers submachine guns and have them rob a bank, with bonus points if there's a police officer inside and for rape.
Bones does this quite often. There has been episodes about competitive arcade gaming, role-playing teens, pony play fetishists, and karaoke singers (with actual former American Idol contestants).
Mostly averted in the episode dealing with black metal, though. Some of the stranger excesses of the subculture are brought to the fore, but Bones's psychiatrist is revealed to have a history in the scene and Booth compares the distaste over it to his dad's distaste for punk. The most significant error they make is that, while virtually everything regarding extreme black metal is true to a degree, the death metal subculture really isn't as violent or cult-like as the Norwegian black metal scene that clearly inspired the events of the episode. Furthermore, few death metal bands wear corpse paint, or use fake names, and only a handful are satanic.
They applied the zero-research attitude to Wicca.
This also gets annoying when Sweets (the psychiatrist) "analyzes" the subculture in question, and ends up pretty much generalizing the entire subculture and assuming everyone who's a part of it thinks and acts exactly the same.
Doomsday preppers, of all groups, were declared freaks. Even Sweets declared them irredeemably freakish. Just being part of a doomsday prepper group makes you a viable murder suspect.
One of the defining examples was "Next Stop, Nowhere," a.k.a, "the punk rock episode of Quincy." In the '80s Hardcore Punk subculture, the episode spawned the slur "Quincy punk," applied to scene members and bands who personified the old Sex Pistols stereotype of the sloppy, antisocial, mohawked/spiky-haired punk rocker. This was at a time when hardcore was about dressing normal, playing tight, and maintaining a positive or at least thoughtful attitude.
In one episode, only one cop on Law & Order had heard of foot fetishes.
The franchise as a whole (The Mothership, SVU, and CI) tends to treat sports fans this way.
One Pushing Daisies episode focuses on a murder at a rent-a-friend agency. The actual customers are portrayed sympathetically, but Ned eventually decries the whole enterprise as useless, because while the patrons may enjoy it for a time, "deep down they never stop thinking of themselves as weirdos who need to be fixed".
Most crime shows had a vampire-related episode at some point of time.
Criminal Minds even did some namedropping by referencing Twilight. At least they didn't portray the subculture as the cause of the culprit's murderous ways; it was made very clear that the killer was suffering from a rare mental illness that provoked obsession with blood-drinking, and had likely had it since childhood.
Hilariously, an episode of Buffy the Vampire Slayer did this with a vampire wannabe cult (mind you, in a show where vampires were very real). At one point, Angel (the resident good guy vampire) is complaining about how these kids know nothing about vampires, don't know how they dress... and pauses as a guy walks by dressed exactly the same as him. At the end of the episode, Buffy has to save the vampire wannabes from the real vampires, who mostly just want to kill them and feed off them.
Supernatural also did an episode about vampire wannabes. It starts off as a funny Take That against Twilight, but, this being Supernatural, suddenly gets a lot darker, when Dean discovers the vampires themselves are pushing the recent vampire obsession, to get more willing victims for a vampire army.
An episode of The Mentalist featured a young Wiccan, who naturally came under suspicion when one of her peers was killed in a ritualistic fashion. An especially aggravating case as half the facts spouted about Wicca were blatantly wrong. Contemporary Pagan religions often appear in shows like this, and rarely do the writing staff seem to feel any compulsion to actually research them first.
A sixth season episode used bloggers as the Sick Sad Subculture. Seeing as everyone and their grandmother has a blog these days, seeing it portrayed as a crazy new subculture was... odd. The show wasn't explicit that all bloggers were exhibitionist freaks, but it was pretty clear that the particular patient was taking it waaaaaaay too far (compulsively documenting literally everything except her bowel movements and even leaving her medical decisions up to popular polling among her readers)
Renaissance Faire playacting was held up to the light in another episode from the same season. The POTW was a jousting knight who took the Medieval code too seriously, not taking into account the "king" he pledged fealty to was just a garden variety yuppie douche in real life. The implication was that this extreme attitude is common.
The late-60's revival of Dragnet used the hippie counterculture as a recurring subculture-of-the-week in a number of episodes. The most infamous of these is the "Blue Boy" episode, for its Narmy take on LSD. Joe Friday references in dialogue the notorious urban myth about teenagers tripping on acid blinding themselves by staring at the sun.
One episode had the detectives practically declare an adult had to be a pedophile... because he collected Transformers.
In one episode, several of them express incredulity over the theory cited by a colleague that a man might be gay even though he has a wife.
In another episode, the idea that someone could be bisexual rather than straight-out gay seems to be bizarrely unheard of, sparking more astonishment from the characters.
In Nip/Tuck the client/patient of the week was often part of some strange subculture.
The whole point of the MTV reality show True Life seems to be to subvert this, as they visit the lives of people involved in various subcultures regularly. More often than not, though, it winds up as a double-subversion.
The Wiccans featured in True Blood's fourth season are presented this way, as if the entirety of the writers' research was browsing an occult shop for twenty minutes. The rather painful mispronunciation of "Samhain" does not help.
Toyed with in the Futurama episode, "Where No Fan Has Gone Before"; the antagonist Melllvar is an obsessive Trekkie, and the episode goes on to explain that in the past, Trekkies became their own religion and started a devastating war that forced the show itself to be banned.
Castle has, so far, largely subverted the "horrifically stereotyped" part. Probably due in part to Nathan Fillion being a fan of several of the subcultures that have appeared so far. And him having a sizeable chunk of fans who are in one or more of those subcultures. The show actually tends to go the other direction with it, such as when Beckett was suspiciously knowledgeable about the BDSM scene, or Castle's fanboying over the whole concept of Steampunk.
Frequently on King of the Hill, Bobby would get involved with a strange new crowd, much to Hank's dismay. Even when the group is benign and Bobby picks up a constructive hobby, Hank will still stop at nothing to pull his son out of it in favor of something "normal."
Recent episodes of The Simpsons have been using this trope heavily, featuring subcultures and lifestyles that have gained prominence in the few years leading up to the episode, in an attempt to keep the show relevant.
Monk has episodes where Monk investigates murders committed in different subcultures: "Mr. Monk Goes to a Rock Concert" has the music industry, "Mr. Monk and the Rapper" involves rappers, "Mr. Monk and the Naked Man" has nudists, "Mr. Monk Takes a Punch" involves a hit put out on a professional boxer, "Mr. Monk and the Garbage Strike" and "Mr. Monk and the Candidate" involve city politics, "Mr. Monk Goes to Vegas" involves casinos, and so-on.