Decontamination Chamber

Wendy: Showers?

Ida: Yeah. Decon protocol, honey. That's what you get for being made of meat.

—The Middleman, "The Clotharian Contamination Protocol"

A standard for any setting where there's a chance of contamination, usually by an alien virus. Also, since decontamination usually means stripping and scrubbing, it also gives a chance for Fan Service and/or humor.

Examples of Decontamination Chamber include:

Anime and Manga

In episode 13 of Neon Genesis Evangelion "Lilliputian Hitcher", Shinji, Asuka, and Rei must enter one of these (naked and at the same time) in preparation for a test of their Eva's systems, much to Shinji and Asuka's dismay. Rei, of course, doesn't seem to be bothered.
- Rebuild 2.0 has a scene as well. When the gang visits a maritime life preserve, they have to go through a very rigorous decontamination process involving x-ray booths, hot showers, cold showers, hurricane-strength drying chambers, being completely submerged in disinfectant all to keep the purified water tanks that way. This despite allowing visitors to the open roof of the complex, basically defeating the point. As always, Rei is completely impassive while her peers scream through the whole process. Unlike the above example though, this time everyone is allowed to keep underwear during decon.

Film

The Andromeda Strain (1971) had an extended Decontamination Chamber scene while the scientists were entering Project Wildfire. It was done to prevent any Earth microbes from contaminating the facility and interfering with their experiments.
The radiation scrub-down is featured in Dr. No (including Ursula Andress in Nude-Colored Clothes) and in Indiana Jones and the Kingdom of the Crystal Skull.
The human cities in Final Fantasy the Spirits Within have a decontamination protocol against the deadly phantoms haunting the outside world, Aki BSs her way around it to hide the ghost contained in her.
Silkwood

Literature

Anne McCaffrey and Mercedes Lackey used this in The Ship Who... Searched: the planet on which the Cades are working at the opening of the story is a Mars-type planet with an atmosphere that humans can't breathe, but which can support other types of life. Unfortunately. Decontamination procedures are required whenever someone comes in through the airlock. Readers are treated to some graphic depictions of what can happen when decontamination procedures prove inadequate or aren't followed properly.
Briar's Book, or The Healing In The Vine as it's known in the UK, features a horrible plague, and Briar and his teacher Rosethorn are exposed to it and have to set up briefly in a plague house, trying to tend the dying. People who haven't been exposed yet can go in and out in special magic-treated clothes, scrubbing themselves and burning the clothes when they leave. Very unsexy. Also, one of Briar's housemates assists in the search for the cure, which involves handling the distilled disease inside of a greenhouse, and lots of decontamination both going in and coming out. Also very unsexy.
Lensman. It's mentioned that the Galactic Patrol base on Trenco has to have thorough decon procedures as the native life is so voracious that the base has been depopulated several times; even the smallest form of life rapidly reproduces and eats everything else.
The Strain: Eph and Nora have to strip and decontaminate before investigating the plane. Eph notes the process of sterilization reduces sexual tension.
The novelization of Command and Conquer 3 describes, in detail, the decontamination procedures when you have to travel from a yellow zone back into a blue zone. It includes, but is not limited to, having your clothes incinerated; being sprayed with a substance that hardens and is then ripped off, along with a layer of skin; and taking a pill that causes you to vomit, urinate, and have a bowel movement in rapid sequence ... and having THAT examined for Tiberium contamination ... before you're allowed in.
Commonplace in Newsflesh for any reporter who has had to go into a zombie-infested location.
Speaker for the Dead features a decontamination chamber between the pequeninos' land and the human city. It sprays unpleasantly caustic fumes, causing coughing and watering eyes.

Live Action TV

Happens to Sydney Bristow in Alias after she almost gets dissolved by acid (the suit is this close to failing when Sark switches it off in return for Sydney helping him bump off Sloane--apparently).
In the second season of Heroes, Peter Petrelli is restrained, stripped naked, and forcibly showered in a bad future by men in decontamination suit as a precaution against a air born disease.
Doctor Who, "New Earth." Built right into the hospital elevators, and a massive plot point at the end.
The "biosphere" episode of Eureka. Almost always played for awkward sexual tension moments.
As shown above, used in The Middleman with great glee. Or, as MM himself said, "Quit your grinnin' and drop your linen!"
Pushing Daisies, oddly enough, in the episode about scent.
In the Star Trek: The Original Series episode "The Naked Time", the transporter room was shown to have the ability to decontaminate the outside of isolation suits with some sort(s) of radiation. Of course the sort of radiation that would do that would also, at the least, damage the skin of the people in the suits unless the suits blocked the rays...and unfortunately the idiot who beamed down with Spock had taken off a glove, been contaminated, and then put the glove back on- thereby making sure the rays would do nothing (not that they'd have done anything against an infection within someone's body anyway).
- Later Star Trek series's mention that the transporters do this themselves. It's used as a plot point in one episode.
Star Trek: Enterprise, existing in a time before transporters with biofilters, had the decontamination room, which seemed to exist mainly for Fan Service reasons. For some reason though two men sent on an away mission would never end up rubbing decon gel on each other.
Averted on ER, when a benzene-exposed Carter is hastily stripped and hosed down in a prefab shower-stall in the ambulance bay. Not played for Fanservice, either.
Kate and Tony spend a few nights in a special quarantine chamber on NCIS after a possible exposure to terrorist-delivered plague. They debate whether the blue lights in the chamber actually destroy bacteria, or are merely there as a placebo to ease their fears. This would be an aversion, except for the Shower Scene involving them and Gibbs earlier in the episode.
The X-Files. In "One Son" Mulder and Scully go through decontamination at the Center for Disease Control facility at Fort Marlene, including a Shower Scene where they're seperated only by a shoulder-high wall. No words are exchanged, though even Celibate Hero Mulder can't stop his eyes flicking downwards when he and Scully turn to face each other.
Happened to Sarah Connor on The Sarah Connor Chronicles. It was portrayed realistically and looked extremely uncomfortable. It turned out that her boss faked her radiation test in an attempt to intimidate her.
This happened to Sara and Greg on an episode of CSI leading to a hilarious exchange between the two once they're back at the lab that Grissom hears out of context. The look on his face is priceless.
Psych, in the episode "Death is in the Air." Lassiter and Juliet get the hose-down as well as Shawn and Gus. Played for laughs, like everything else in Psych.
Sanctuary had this happen to Dr. Magnus in an alternate future with a Zombie Apocalypse.
In The Walking Dead, the CDC scientist uses one when he spills a caustic chemical then gets them on his suit. He runs to the chamber then realizes too late and watches in horror as the lab is torched, destroying his one good sample of the zombie virus.

Real Life

The Lunar Receiving Laboratory, used to decontaminate/quarantine Apollo astronauts returning from the Moon. Completed in 1967, it may have inspired Project Wildfire in the original The Andromeda Strain novel (1969).
Underwater and space situations tend to have decompression chambers that serve a similar dramatic purpose.
Work in any kind of clean room and you'll be decontaminated in and/or out with a variety of stuff, depending on what is in the work area.
Anyone who is exposed to radiation is scrubbed down. Instructions for emergency workers after a nuclear accident involves shaving off all hair (if possible), removing and burying all clothes and jewelry, scrubbing with a rough brush. This is to reduce the damage done by fallout and the radioactive dust and grime that might be covering you. It's one thing to be exposed to radiation for 2 minutes. It is another to have a bit of radioactive grime in your hair bombarding your skull for hours and hours.
Many modern hospital emergency departments have "decon rooms" designed to handle decontamination from nuclear, biological, and chemical exposures for limited numbers of patients. (Mass casualty incidents still require breaking out the old-school decon tents). These rooms are equipped with multiple high-pressure showerheads and hoses, a negative-pressure air filtration system separate from the rest of the hospital, and drains that run to separate holding tanks rather than to the public sewers. Emergency response protocol doesn't use or advocate specialized solvents or scrubbing skin with brushes anymore; 95% of decontamination can be accomplished simply by removing all clothing and a thorough wash with soap and water, and the old "shave and scrub" procedure actually worsens most cases of NBC exposure by creating breaks in the skin for the toxic agent to penetrate.
Field saunas were used as this during World War II. Soldiers would collect lice like...well...lice and it was a useful means of cooking the lice to death.

Tabletop Games

Paranoia supplement Acute Paranoia. In the Botbusters adventure, an evil Comp Node tries to get a group of robots to go through a Decontamination Chamber. It's actually a trap to spray them with a disease that will kill many clones in Alpha Complex.

Video Games

There's a couple of labs toward the end of BioShock (series) with decontamination chambers for entrances.
In Dead Space, Isaac frequently runs into decontamination lockdowns. When that happens, the Necromorphs come out in force, and the quarantine is only lifted once Isaac puts them all down.
Half Life: "If you're ever in trouble, just step into one of these decontamination booths and hit the big red button. It's supposed to kill micro-organisms but, heh, believe me- they work on the big stuff too."
Space Quest uses a decontamination chamber exactly once in the entire series: at the beginning of the second game. Every other time that Roger goes on a space walk or visits a strange planet or goes on some crazy adventure involving goopy mutants, he apparently doesn't come into contact with anything contaminating.
- Anything contaminating he comes into contact with is likely to cause a Game Over in short order, such as the mutating goop from the fifth game.
A door in Time Splitters: Future Perfect won't open unless you run yourself through a decontamination shower.
In Mass Effect the Normandy's airlock also functions as a decontamination chamber. A beam of light sweeps over the characters as they wait to enter and exit the vessel, while the soothing voice of the ship's VI announces 'Decontamination in progress'. The characters are in full armor during the process. Once they are inside, they've taken the armor off however, implying that changing clothes is part of the process.
- Quarians are really big on decontamination: visitors to the Migrant Fleet are not even permitted to take their environment suits off while on board. Even with the Normandy's decontamination airlock, Tali warns her fleet prior to docking that the ship is "not clean" and requests a decon team to meet them at the airlock.
Doom 3 had Decontamination Chambers near some (but not all) experimental teleporters. They also have a bio scan system before you enter Mars city proper.
The Deep Six mission from Max Payne has you going through one of these. The guy who helps you get through is killed by Horne's mercenaries shortly after helping you through.
Champions Online features a hastily implemented Decontamination Shower in the overrun base in the Desert Crisis zone, one of two possible starting zones after the tutorial zone, and before the primary zones.
In the inevitable sewer mission in the game Dark Forces, the briefing mentions having the decontamination shower warmed up a ready when you return.
System Shock 2 contains one, but it's only partly functional because you have to stand directly under the spray.
Dwarf Fortress has "contaminants" ranging from useful but annoying mud to contact poisons quickly and hideously killing anyone, and they all stick to the boots of any passing dorf. These guys aren't smart enough to go wash before they got the whole town splattered with this crap, so frequently visited places have to be protected by measures like shower entrances, whether in trap-like setup or constantly pumping.
Done in Quake IV after coming aboard the starship.

Web Original

In the Whateley Universe story "Christmas Crisis", Tennyo had to go through one after surviving a nuclear bomb. Since she looks more like Ryoko than anyone ought to, the soldiers around her who weren't worried about her dying of radiation poisoning were really looking forward to seeing it.

Western Animation

The decontamination of monsters touched by children in Monsters, Inc. plays this for laughs.
It can be argued the Jacques the shrimp from the movie Finding Nemo is the dentist's aquarium's equivalent of a decontamination shower.
Used in Transformers Animated by Sentinel Prime to pick on the Autobots who have been living on Earth by removing possible organic contamination.

Comics

Tony Stark the last normal human alive in Earth X sealed himself away and only let his robot Avengers in after getting decontaminated.