Sometimes a Knight Errant or The Drifter can't get the job done alone. So what do they do? Why, gather a group of likeminded individuals, of course. The Order is a group of people come together to further some aim, whether it's to accomplish a specific goal or in support of a more general set of ideals, which are usually written down in its Code. It is usually a highly exclusive organization — you cannot simply join, you must be recruited (or at least pass a difficult application process of some kind). However, despite these high standards, The Order can vary widely in size and influence. It may be a small, elite group of adventurers, or it may be an army-sized power unto itself with its own dedicated support staff and base(s) of operations.
The Order is often grounded in an Ancient Tradition, which may or may not be public knowledge. Many fictional Orders also train their members in the use of some Secret Art — in which case they are likely to only recruit those with the potential to use it. The Order is itself often (but not always) a part of The Church, making them Church Militants. This is probably a holdover from real life knightly orders, groups dedicated to the advancement of Christian interests and officially acknowledged by the Catholic Church. Similarly, you can expect many fictional Orders to have a distinctly chivalric flavor — even if the setting isn't otherwise medieval.
Orders can be secret or public, good or evil, but much like The Kingdom, good Orders show up far more often in fiction. Heroic Orders are likely to also be Heroes R Us, and dead Orders usually inspire Order Reborn plots. Paladins are usually part of an Order. If their purpose is protecting an ancient MacGuffin or other secrets they're an Ancient Order of Protectors. Compare with Avengers Assemble.
The "Jusenkyo Morals Committee" from a filler episode of Ranma ½ are a comically inept take on this concept. Their paladin Kenny the Enforcer's own Jusenkyo curse from the spring of the drowned pacifist Buddhist monk proves to be an Achilles' Heel.
The Sacred Order of Saint Dumas from Batman comics.
DC Comics' Atomic Knights, a knightly order established After the End (possibly in the same future as Kamandi) by Sgt Gardner Grayle to protect the remains of civilization from the Black Baron. Later revealed as All Just a Dream, and later still Grayle set up a real order of Atomic Knights in the ruins of Bludhaven.
The Blood of the Ghost Rider comics fought alongside the spirits of vengeance in the past. The Caretaker is a survivor from this order, which is why he knows so much about the Ghost Rider.
The Medjai in The Mummy Trilogy, whose job seems to be to protect all the potentially world-ending crap that the ancient Egyptians left lying around. There seems to be just the one guy in the first movie, but in the second they're upgraded to The Cavalry against the resurrected army of Anubis.
The Michaelines, named for their patron Saint Michael the Archangel, are a military order prominent in the Camber trilogy. They are presented as a cross between common notions of the Templars and the Jesuits: wealthy, powerful, and adept at all forms of combat (including intellectual). Their membership was mixed human and Deryni, with the Deryni leading the others in quasi-arcane meditations. Camber's son Joram was a member, as was his late-life alter ego Alister Cullen (Vicar General of the Order). The Michaelines were suppressed by the the regents circa 918, and many members fled into exile with the Knights of the Anvil.
The Knights of the Anvil, or Anvillers, take their name from their home region, a harsh environment southeast of Bremagne called the Anvil of the Lord. A military order with a reputation for stealth, the Anvillers were influenced by many cultures, Muslim as well as Christian. Members have small crosses tattooed on their bodies in remembrance of Christ's wounds when they take final vows; Sir Sé Trelawney displays those at his wrists (and jestingly refers to the others) on a visit to Alyce de Corwyn Morgan in Childe Morgan.
The Order of the Phoenix from Harry Potter series is a rather small example of limited scope (a dozen or so people at any one time, focusing on opposing Voldemort). Their evil counterpart are the Death Eaters, Voldemort's inner circle.
The elite intellectual organization residing in Castalia, called simply "The Order", in The Glass Bead Game.
The Dresden Files has the Knights of the Cross, a group of three men who each were given swords that are said to have one of the nails of Christ's cross embedded on it. This gives them the ability to fight off forces of evil, and they've helped Harry Dresden many a time in defeating dark supernatural creatures. Interestingly, only one of them is truly Catholic, and he's easily the nicest, least Church Militant person ever; out of the other two, one got converted by mistake, and the other one is a skeptic who believes heavenly creatures — including the archangel that gave him his sword — can just as easily be Sufficiently Advanced Aliens.
There's also the White Council, which could fit the description. Unfortunately, among the senior council, the Merlin is a pretentious ass, Ancient Mai usually comes across as a horrid bitch, and Gregori Cristos is, in Ebenezar's words, an unpleasant bastard.
In L. Jagi Lamplighter's Prospero's Daughter trilogy, the Orbis Suleimani keeps mankind ignorant of the existence of magic. That way, instead of resorting to evil spirits, we resort to science and so live much better.
A Song of Ice and Fire has numerous examples, ranging from the Night's Watch (dedicated to protecting Westeros from the threats in the North) to the maesters (who are dedicated to study and the gathering of knowledge), to the Kingsguard (a group of exactly seven knights, who act as the king's Praetorian Guard).
The "League" the main character belonged to in his youth, in The Journey to the East by Herman Hesse.
Live Action TV
The Watcher's Council on Buffy the Vampire Slayer. Since there is only one active Slayer at any time (in theory), the show was always vague about what the rest of the organization got up to. It didn't help that some of their actions bordered on Knight Templar, especially in season three, which saw Giles being fired halfway through and ended with Buffy telling them she was doing things her way from now on. They were a bit more helpful in season five, but their contribution to season seven was to be blown up.
Quentin: We're not in the business of fair, Miss Summers, we're fighting a war.
Giles: You're waging a war. She's fighting it. There's a difference.
The Order of Aurelius, which all the main vampires (Angel, Spike, Darla, Dru, The Master) were essentially part of, due to it being a bloodline kind of thing, probably also counts.
Myth and Legend
King Arthur's Knights of the Round Table, one of the most famous knightly orders in the Western world.
Forgotten Realms has a lot of gods sponsoring paladins, each having one or more paladin order to his name, divided by regions or specific tasks — such as Knights of Samular, dedicated mainly to hunting down some dangerous artifacts around Sword Coast. "Mundane" knightly organizations may be even more numerous.
The city-state of Ravens Bluff alone has its knighthood split into 8 specialized orders. Initiate-level Order of the Golden Rooster (concerned with their and city's prestige and appearance), then secular orders of Griffon (martial might), Dove (diplomacy, non-violent problem solving) and Hawk (intelligence, undercover investigations), then higher-ranked religious orders — Keepers of the Mystic Flame (magic threats), Right hand of Tyr (justice) and Phoenix (The Undead and pesky extraplanars) and the elite order, Knights of the Raven.
The Harpers are a widespread secret society that seeks to oppose evil in all it's forms, they're less organized and less formal (members meet rarely and irregularly at gatherings that resemble fey parties more than anything else, and all it really takes to join is the sponsorship of an established member or two) than most examples of this trope, but they're certainly exclusive enough and goal-oriented enough to qualify.
The various magical groups in Shadowrun fill this role for people with the potential for magic. The exact perks gained depend on the group, but they can all help mages become initiates, which gives them greater power and abilities.
Most other Space Marine Chapters, the Inquisition, the Adeptas Sororitas, most Eldar Aspect temples, the Incubi cults, and the Harlequins/White Seers also qualify to one degree or another. The Deathwatch is slightly more of a Legion of Lost SoulsIN SPACE!, though.
Warhammer, many Imperial Knights belong to a certain order, they are either Templar Orders who venerate a particular god, or are Secular Orders who honor most gods equally.
BIONICLE: The Hand of Artakha and its successor The Order of Mata Nui
The Grey Wardens of Dragon Age were formed to guard against the Darkspawn. The Circle of Magi exists to train and control mages... and the Templars exist to hunt mages outside the Circle's control. Dragon Age's mages can be dangerous.
Not to mention the Ben-Hassrath, the Seekers, the Silent Sisters and the Legion of the Dead.
The Elder Scrolls series has quite a few, as benefits its medieval fantasy setting. A few of the more relevant ones:
The Blades, the personal bodyguard (and spies, and general secret agents) of the Emperor. The Order of Talos, a religious order worshiping Talos (aka Tiber Septim, the founder of the Imperial dynasty of the Third Era) overlaps quite a bit with (but is technically distinct from) the Blades.
The Dark Brotherhood, an order of assassins that worship Sithis and a being known as the Night Mother via contract killings. New members are recruited via a mysterious hooded man (or woman, in the case of Skyrim) appearing to them while they sleep the night after the first time they murder an innocent.
The Thieves' Guild, which provides fences for its members to dispose of stolen goods. To join, you have to find your way to a secret recruitment meeting, then beat out other potential recruits in a test of thievery. They forbid their members from harming targets during jobs.
The Oblivion DLC "Knights of the Nine" adds a sidequest where you can revive the eponymous order, dedicated to the ultimate defeat of a particular Sealed Evil in a Can. It ultimately consists of nine knights and a handful of support staff, based out of a small fort in the wilderness.
The Skyrim DLC "Dawnguard" has the dawnguard, an Order Reborn that fights vampires when the Jarl of Riften's son turned into a vampire.
Order of the Hammer, a.k.a. Hammerites, in the Thief series.
Order of the Sunspears and Order of Whispers in Guild Wars.
The Spectres in Mass Effect series are a somewhat atypical Space Opera example. They are a very exclusive organization (naming a person a Spectre requires unanimous decision by the Citadel Council, so Shepard was the first human to gain the title) pledged to the service of the Council and "there's no such thing as a 'former Spectre'". The atypical part is that they tend to operate alone (or with their own assembled teams) and without much support from the organization itself, though they do have access to stocks of rare and highly advanced equipment. Also, they can requisition Council resources as necessary, e.g. extranet bandwidth.
The Order of the Flame from Drakan, though it's more of an Order Reborn, since Arokh is the only living dragon throughout both games who can be considered a member.
The Brotherhood of Steel from the Fallout series is one of the larger examples, as one of the major powers in the setting. Though they use powered armor and BFGs instead of swords and shields, they have a deliberate chivalric flavor — their soldiers are "knights" (and elite ones "paladins"), their scientists are "scribes", their leaders are "elders", etc. Their Ancient Tradition is the preservation of technology and technical knowledge in the post-apocalyptic wasteland, often to the exclusion of helping people.
Fallout 3 has the spinoff Columbia chapter, whose Cool Old Guy leader has shifted priorities from collecting technology in the D.C. Wasteland to containing the local Super Mutant population. This was technically okayed by the main Brotherhood leadership... but they stoped sending reinforcements and supplies immediately thereafter, essentially making the Brotherhood (Columbia chapter) a separate faction. The Columbia chapter eventually spawns its own spinoff, the Brotherhood Outcasts, who adhere to the main Brotherhood's "technology is more important than anything else" philosophy, and left the now Lyons' Brotherhood of Steel to follow it.
Fallout 3 also has the Regulators, a group of Vigilante Men who are essentially The Sheriff in a setting with no government to give them legitimate authority — so they take it into their own hands. If the player ends up on the evil end of the Karma Meter, they'll become a Random Encounter trying to kill him.
The Knights of the Silver Hand from the Warcraft setting were founded by the first paladins. It had quite a few members at one point, but was largely wiped out by Arthas after his corruption. It was later reformed by Tirion Fordring, and then merged with the Argent Dawn to form the Argent Crusade.
The Ultima games have the Order of the Silver Serpent, operating out of Serpent's Hold. Exclusive to Ultima Underworld are the Knights of the Crux Ansata.
Both ''Duty'' and ''Freedom'' in S.T.A.L.K.E.R. consider themselves this, both being organizations determined to prevent the Zone from spreading, but engaged in a war over how to do it. (Duty believing in completely sealing off all access and keep anyone from meddling with it, Freedom wanting to make the area safe enough to allow to allow international researcher to study and reverse or contain the Zone). Monolith might also count in some ways, though they are more like an evil cult of brainwashed madmen.
Another use of the trope name verbatim, The Order from Strife. Described quite adequately in the manual as a religious dictatorship that uses cybernetic augmentation and advanced weaponry to conquer the populace. And the that religion involves an evil alien that arrived via the same comet that spread The Virus that caused assorted death, mutation, and a tendacy towards revering The Entity.
Rumors of War brings us the Order of Orion, which falls somewhere between Heroes R Us and Weird Trade Union. We aren't sure what they do exactly, except that they recruit heroes, fund exploration and mining operations, and have some hand in maritime trade. We don't know the conditions under which the cast were recruited, and we don't know what function they serve in the Order.
The eponymous Order of the Stick is not an example itself; however, the Sapphire Guard may be considered to be one.
Despite never being called such, the Justice League fits the description. Dedicated to maintaining world security and justice and highly exclusive (so much that Aquaman was the only superhero to join the original lineup until Unlimited—and only in an alternate timeline). Even after they expand (by invitation only), they maintain strict membership policies, as Huntress' example demonstrates.
The Order of the White Lotus from Avatar: The Last Airbender plays this straight. A secret society dedicated to the martial arts and pai sho, they originally resembled a sort of cross between a social club and an underground railroad. They rose to prominence during the end of the Hundred Year War and, by the time ofThe Legend of Korra, had shed the "secret" part and apparently much of the exclusivity of their membership requirements and become a Red Shirt Army in the service of the Avatar.