The PKC in Legend of the Galactic Heroes fits the bill in the case of the Free Planets Alliance. Though it's later revealed that the militia was supported by Trünicht, with at least a good chunk of them members of the Earth Cult.
The Free States in DMZ are said to be a conglomeration of militia-type groups, and are said to be more of an "idea" rather than a geographical entity, much in keeping with the guerilla-style behavior of many militias. The hick element is also mentioned when a former Free States soldier mentions how, while serving with them, he'd never before seen as many "pissed-off rednecks".
The bad guys of The Crow: Flesh and Blood are a group of farmers connected to an anti-government militia. Federal conservation officer Iris Shaw runs foul of them when she comes across them poisoning coyotes, and after a confrontation with them, they blow up the land management building where she works, killing her and her unborn child. When Iris comes back as the first female Crow, she wreaks vengeance on each and every one of them.
The 2000 movie Militia features a fascist militia stealing anthrax missiles.
Parodied in The Stuff, with a group of these guys help the heroes (or rather, they get tricked into helping the heroes after being told the Stuff is a Communist plot).
The Happening. When a news report claims that the events of the film are the result of a CIA bioweapon test gone wrong, a group of obvious militia types with "I Knew It!" expressions are seen loading an arsenal of weaponry in their garage.
Von Jackson and his border vigilantes in Machete, even though they're secretly patsies to a Mexican drug lord.
The antagonists in The Postman, which takes place in a United States that collapsed after a civil war.
A right wing militia group is one of the one the bad guys in Blues Brothers 2000 (more or less filling the role the neo-Nazis played in the original film).
The bad guys in the 1998 Steven Seagal film The Patriot (in which Seagal plays an immunologist!).
In Executive Orders, two members of a militia group decide to assassinate President Ryan with a cement trunk bomb. They make their way across the country, hindered by the virus outbreak caused by the real Big Bad, until they are arrested with no consequence before they even reach Washington. Being generous to Clancy, they might well have succeeded had the Iranian bioterrorism plot not forced them to stop at a motel for days while their bomb "ripened".
Averted in The Survivalist, a 1980s action-adventure series by Jerry Ahern, set in a post-World War III United States occupied by the Soviets. The author goes to great lengths to avert the popular strawman of survivalists being paranoid, fascistic racists.
The Turner Diaries has a particularly extreme version of these guys as the heroes, and was written for exactly this audience by white supremacist leader William Luther Pierce.
On the other hand, it also gives a negative portrayal of such groups, though not for the same reasons as most depictions. In the story, the anti-government John Birch Society types who take over northern California turn against the Order, claiming that its goals are ultimately communist. This was intended as a warning by Pierce, saying that white supremacists shouldn't ally with anyone other than their fellow white supremacists even if they have sympathetic politics.
Arthur C. Clarke's The Trigger shows one of these on the defensive. The premise of the book is that the U.S. has invented a way to sabotage guns from a distance, and they think this only makes sense if the U.S. is no longer going to rely on its advantages in gun development — which means to them that the U.S. is about to hand over sovereignty to the United Nations. They're portrayed as somewhat pathetic, but still dangerous to everyone around them as they try to keep their "freedom."
The USA vs. Militia series by Ian Slater deals with a full-scale militia rebellion in America, and it was a very well-equipped militia complete with tanks and jet fighters. And to make matters worse, the war is set while World War Three is still raging.
In The Stand, Randall Flagg was a member of some groups like this, though he'll join any organization that he can egg on into causing trouble.
These are the main villains of the Lee Child novel Die Trying.
These are the villains of the Dale Brown book A Time for Patriots.
In the epilogue of the Animorphs series it's revealed in an aside that since aliens have become public knowledge a number of these groups have sprung in the world. Disappointingly, they're not explored in great detail due to the Animorphs quickly leaving for space.
In Night Passage, the first Jesse Stone novel, the town of Paradise, Massachusetts has a group of these called the Horsemen, whose members include several people on the local Select Board. They wind up murdering the former Chief of Police when he catches on to their plan to stockpile weapons and take on the US Government. Then they hire Jesse after he shows up drunk to his job interview, thinking he'll be too incompetent to figure out what they're up to. They're wrong.
It's hinted in World War Z that militia groups caused trouble for the US during the Zombie War, feeling that America had become tyrannical as a result of the wartime measures imposed to fight the Zombie Apocalypse. The government was forced to clamp down hard; one group that had taken over the Black Hills was met with the only use of tanks by the US military during its push east.
In Shock And Awe, one of the protagonists is an FBI agent undercover with one of these whose group gets roped into the Big Good's plot.
Live Action TV
Parodied by Mr. Show with the character of Mountain Dougie, who tries to secede from the United States — and succeeds. He then creates a flag and currency for his new nation of 'New Freeland,' but is enticed by the wonders of America (they have food there) and emigrates to the US.
When the crew of Voyager travel back to the past, they run afoul of a few paranoid survivalists who they think they are government agents. They get taken out by the Doctor, who stuns them with his phaser after their bullets pass right through him.
One irony, intended or not, is that the crew members they capture are Chakotay and Torres, who themselves worked with the militia-esque Maquis before the series began.
Jim Backus (in what must have been a career lowlight for him) appears as the leader of one of these militias in the MST3K episode Angels Revenge.
Another trope fully embraced by Law & Order — especially during the late 90s. One episode called "Nullification" had a group of so called "American Patriots" claim an armored car heist (in which a guard was killed) was an act of civil disobedience akin to the Boston Tea Party. They managed a mistrial because of one disaffected juror whom McCoy had sniffed out, but refused to dismiss because he didn't want to win by working the system like the defendants were doing.
Subverted in Criminal Minds. When they go after one of these groups it turns out that a cult has taken over their compound and when the track down the original leader he's much more reasonable than expected.
Similarly, although the militia in another episode are portrayed as racist and antagonistic, they also ran the killer out of town for abusing his wife and it's one of them who shoots the killer in the end.
After Kim Bauer escapes a random cougar on 24, she runs into one of these, who takes her prisoner.
One episode of Diagnosis: Murder featured a militia group trying to separate the US West Coast into a state for whites, complete with the We Are Everywhere threat and a stolen nuke.
Leverage: "The Gone-Fishin' Job" features as its mark a debt collector using a list from the IRS to scam people out of cash that he's using to finance his own private revolution complete with possible truck bomb.
Team Gibbs from NCIS finger a militia group for the theft of military weapons ("Split Decision") in the first season.
In "Brig Break", the Gunnery Sergeant in charge of the brig uses a right wing militia group as a decoy to keep base security busy while steals weapons for Saddam Hussein's Iraq.
In "Vanished", a right wing militia group called Freedom Brethren kidnaps the wife and child of a F-14 pilot, and convinces the aviator to bring them the aircraft and to shoot down a certain civilian airliner. If demands are not fulfilled, the wife and child will die.
In "Rivers' Run" Harm and Mac defends Navy Seal Lt. Curtis Rivers in a kangaroo court under the common law, as interpreted by anti-government separatists in West Virginia.
Jim Rockford goes against a group of these in The Rockford Files. When they are arrested for murder at the end of the episode, they behave as though they are prisoners of war.
Rick Flag of Smallville has definite shades of this, believing the government is out to round up and kill superheroes and masked vigilantes. The comparison is made even more obvious by his constant placement of the American flag on his weaponry, his recitation of the ''Star Spangled Banner'' as he prepares to blow up Lois' father, and the huge flag blowing behind his head when he declares war on the government.
The sad thing, however? His fears are turning out to be justified.
In Breakout Kings, the runner in the episode "Like Father, Like Son" is a member of a militia, the Patriotic Front.
Michael, Sam, Fi and Jesse have to rescue an ailing boy from a militia compound run by a Phony Veteran in the Burn Notice episode "Besieged".
An earlier episode has Michael (under duress from Gilroy) negotiating the purchase of a BFG at a neo-Nazi compound. Michael poses as an apolitical Arms Dealer so as to not give the racist scum any ideas that he was supporting their evil cause.
MacGyver: Mac takes on a neo-Nazi group in "The Seven Per Cent Solution".
An episode of Jake 2.0 had one such group kidnap the titular character's younger brother by accident. Unfortunately, the group's leader's fanaticism causes the death of his son.
The Eric Bogle song "Keeper of the Flame" is about the paranoid rantings of a right wing militia fanatic.
In the d20 ModernUrban Arcana setting, there is the Fraternal Order of Vigilance, a militia with a legal front engaging in acts of violence motivated by Fantastic Racism against shadowkinds (i.e. everyone who is not human, including perfectly peaceful elves or blue collar dwarfs.)
The Menace Manual sourcebook has a potentially non-villainous example with the ostensibly anti-fascist 25th Freedom Brigade, who can be either a help or a hindrance to the player characters. As with many other examples, they are very anti-government, comprised mostly of disenfranchised patriotic veterans, and dangerously hostile to those that trespass on their land.
Grand Theft Auto: San Andreas features one mission where CJ must sneak on a farm owned by a Waco-esque group in order to steal their combine harvester for The Truth. They shoot at him on sight — although CJ is trespassing with the intention of committing theft, he barely steps foot on his property before they start firing. Also, they shout racial slurs at CJ and clearly enjoy hunting him down. But once you actually get to the harvester...
In Grand Theft Auto IV's DLC episodes, talk radio host "John Smith" on WKTT (a parody of Alex Jones) is one of these, spouting exaggerated versions of conspiracy theories popular on the radical right. A good number of his callers also fit this mold — in one instance, he hangs up on a man who is praising Adolf Hitler not because he disagrees with him, but because he doesn't want to get fined again (implying that this isn't the first time that such people have called in). There's also his guest at the end of the show, Abigail Grayson, a Crazy Survivalist soccer mom with extra emphasis on the "Crazy".
Grand Theft Auto V has Joe and Josef of the Civil Border Patrol, aka the "Minute Men", a parody of anti-immigrant border militias like the Minuteman Project and Ranch Rescue. While Joe fits the mold to a tee, Josef is a Russian immigrant who barely speaks English, and has a bit of trouble distinguishing between American sayings and British ones; at one point he says he's fighting "for King and Country". It's also implied that Josef is a neo-Nazi as well.
The NSF in Deus Ex were this originally, but by the time of the game the organisation has expanded and attracted representatives of every group hostile to the current US government and/or UNATCO, and as a result, their political stance has drifted quite a bit to the left.
NSF fit this trope all right. The trick is, the government really is using extreme clandestine methods to achieve totalitarian influence. As player learns throughout the game, the level of corruption and greed surpasses even the most haphazard theories of NSF members. You know you live in Crapsack World if Right Wing Militia Fanatic is your good guy.
Counter-Strike features the map CS_Militia and the Militia skin, which is only available by chance on the random skin button.
Sid Meier's Alpha Centauri features the Spartan Federation as a major faction based on this ideology. Yes, of the seven factions (twelve in the expansion) representing what's left of humanity in the future, one is explicitly described as a group of right-wing survivalist fanatics. In a minor subversion, however, their leader is a Latina rather than the stereotypical "angry white man" often associated with the trope. On the other hand, Spartans are pretty collectivist, military survivalists with little or no political agenda.
Subverted in Syphon Filter 3. Teresa's first assignment was to retrieve stolen satellite data taken by a militia, but the NSA team Teresa helps plans to sell it to terrorists and the militia are just unlucky witnesses.
Played with in The Omega Strain, where the main antagonists are Chechen Muslim terrorists, but the first group the player deals with are the French-Canadian Anarchist Libertaire Armee (ALA).
The "America Now" terrorist group in the 11th mission of the career mode in the original SWAT 4.
A group of these appears as enemies in Dead Rising 2. One of them mentions working in border patrol, and they blame the Zombie Apocalypse on liberals, socialists and foreigners (the last one is actually pretty accurate, although it's not like America was completely innocent).
inFAMOUS 2 has the Militia, a group of right-wing extremists who take over New Marais to purge it of mutants (including Cole) and "deviants". They serve as the chief villains for the first half of the game.
The upcoming Rainbow Six: Patriots will have these as the villains.
Left Behind: Eternal Forces has you leading a group of these battling The Antichrist and the GlobalCommunity in the middle of New York. There was a fair bit of controversy over this, with some critics claiming that it was promoting religious violence (notably, Jack Thompson cut his ties to Tyndale House, Left Behind's publisher, over the game), though to be fair the game rewards players for pursuing non-violent means of victory — after all, killing your enemies means that you can't convert them, and it also decreases the morale, or "spirit", of your own units ("thou shalt not kill" and all).
Homefront has you meeting a group of these guys in the fifth level, where you and your group are trying to get a helicopter from them. They're probably the only people in the world who can match the North Koreaninvaders in pure nastiness — they torture and enslave captured enemy soldiers for sport before lynching them and putting their heads on pikes, they try to kidnap your group's female member for "entertainment", and they're not above collaborating with the enemy and turning over resistance members for money.
In Baten Kaitos Origins, this is pretty much Baelheit's Machina conspiracy group in a nutshell. They're hell-bent on overthrowing what they see as the corrupt magical system that rules the world and don't even care if they start a war by doing it. Ultimately subverted, however, as Baelheit turned out to have sympathetic motives - namely the fact that losing his wife and being Forced to Watch as his daughter was savaged by a feral remnant of the Physical God Malpercio led him to despise everything connected to the old gods and their magic.
In the Alternate HistoryDecades of Darkness, the Anglo-Saxon nationalist movement in Britain leads to the growth of the Gaderung (who are based around agricultural self-sufficiency) and the Fyrd (an alternate version of the Boy Scouts), while the government creates the Home Defence Force to protect against invasion. All of these groups rapidly turn into these, especially when Germany invades Britain and law and order breaks down.
Homer Simpson, of all people, shows signs of this in one episode when he hands Bart money printed by 'the Montana Militia', saying 'It'll be real soon enough'. This is, naturally, a throw away joke which is never, ever referenced again.
Herman, an occasionally recurring character who sells military antiques, comes close to playing this trope straight. At times.
What with his talk of the New World Order and trying to secure the MacGuffin for a future war, Silas and MECH of Transformers Prime may be this.