The Marvel Universe has the Watchers, an alien species dedicated to observing everything in the universe without interfering. Further in accordance with the trope, Uatu, the particular Watcher living on Earth's moon, has been known to break or creatively bend his oath of non-interference with some regularity to warn chosen superheroes of that world when 'cosmic' trouble rears its head.
The mere presence of Uatu, without actually speaking a word of warning, is a clear indication that something of cosmic significance is about to happen. And most of Marvel's heroes know it.
On one occasion, the Watchers as a group made a decision to violate their own rules: in Marvel 1602, they help prevent the destruction of the omniverse, which they feel would leave them without anything to watch. In doing so, they condemn all the people and possible people of a certain reality to non-existence, which is one of the reasons why they never interfere.
A DC example might be the Endless from Neil Gaiman's The Sandman, because even though they have interfered with the affairs of humanity for millenia, they aren't evil or good, but just sort of impartial.
This is certainly true early in the series, but by the third book and beyond, a strong argument could be made that they are an Ancient Conspiracy.
Nope: the first foundation is the ancient conspiracy, the second foundation is the safeguard of the ancient conspiracy, and finally we have the collective-consciousness planet/civilization Gaia which is a safeguard of the safeguard of the ancient conspiracy, and all exist because a positronic Xanatos spent 20,000 years following the dying wish of a friend
More accurately, the collective Discordian Cabal. It's implied that the ELF itself is actually relatively young, like its contemporary compatriots. They just happen to know and guard some very old secrets. The actually oldest and most mysterious organization in the book is called A.'.A.'., which is not an acronym of anything; anyone claiming otherwise is an impostor.
The Order of Wen the Eternally Surprised in Discworld.
Marco Soto: We're the most secret society that you can imagine. Newgate Ludd: Really? Who are you, then? Soto: The Monks of History. Ludd: Huh? I've never heard of you! Soto: See? That's how good we are.
Live Action TV
Most of the varied series of Star Trek except Star Trek: Enterprise have as a rule the so-called "Prime Directive". This Directive states that before a society reaches a certain technological level (usually but not always defined as approaching the capacity for faster-than-light travel), that that society is not to be interfered with in any way, or have even the existence of Starfleet, spaceflight, or other worlds revealed to them, lest it change their society. As with most "rules" on Star Trek, this was broken with impunity whenever the plot called for it, or the conditions met with the moral indignation of the observer (usually The Captain), etc...
The Prime Directivesometimes means not interfering with other cultures at all, even space-faring ones at a comparable tech level. It also sometimes mandates hidden interference if it is necessary to keep the other culture existent, and sometimes specifically prohibits it even then. Some Expanded Universe materials attempt to Hand Wave this issue by treating the Prime Directive as a complete mess, drafted in too much haste as a knee-jerk reaction to a terrible mistake, and so so riddled with exceptions and loopholes that Starfleet captains can interpret it to mean whatever the hell they want it to mean.
The AscendedAncients from Stargate SG-1 and Stargate Atlantis have a "strict" non-interference policy with several glaring loopholes (*coughAnubiscough*). They'll adhere to it to the point of just being pricks. Though to be fair, they adhere to it even when the result might be their total anihilation by the Ori, so they must really believe in non interference (or have tremendous faith in the SGC).
Except for Horton's splinter group, who decide to kill them all rather than risk letting any of them get the Prize.
In Doctor Who, traditionally the Time Lords fulfilled this niche, only interfering if something would seriously threaten the timelines. The Doctor was considered a criminal for his desire to interfere with the other civilizations. Of course they started to experience some serious Motive Decay during the Last Great Time War.
The Keepers in the Thief series claim to be this ("Propaganda is Written by the Winners. History is written by the observer.") but in reality, often start meddling in worldly affairs themselves (preferrably, with Garret's hands).
Examples of Aiding
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The Hieda family in Asagiri no Miko protect against demonic forces and assist the Amatsu family in sealing Yagarena.
The Fraternity in the film version of Wanted, whose job is to assassinate those decided by fate to prevent a more horrible event from occurring.
Now You See Me: The Eye , a group dating back to Ancient Egypt dedicated to protecting true magic, are orchestrating the Four Horsemen's performances as a way to test them for membership. Dylan turns out to be a member, and by the end, the Horsemen are in.
The genuine Middle Ages Gaelic religious movement Céli Dé (Companions of God) seves this role in Stephen Lawhead's Celtic Crusades trilogy, surviving to the present day as the Benevolent Order.
Robert A. Heinlein's short story Lost Legacy. A benevolent secret society of people with psychic abilities lives under Mount Shasta. Their membership has included Abraham Lincoln, Ambrose Bierce, Mark Twain and Walt Whitman. They help the protagonists refine their mental abilities and fight the opposition group that wants to keep humanity ignorant.
David Weber's Safehold series has the Brotherhood of St. Zherneau's, a monastery that is the only keeper of pre-Safehold knowledge besides Merlin Athrawes. Because of the power of the Church of God Awaiting, they have kept in the background and paid lip service to them all the while gradually moving the kingdom of Charis towards being able to reveal the Corrupt Church's origins as a Path of Inspiration.
In the short story "The Splendid Source" by Richard Matheson, the hero discovers that an ancient fellowship makes up and spreads most or all of the world's risque jokes. (Ernest Hemingway, alive at the time the story was written, is shown to be a modern-day member.)
"That is history's secret," rejoined the Dean, "veiled behind time's opacity. Our venture does have its honored past, however. Great men have graced its cause — Ben Franklin, Mark Twain, Dickens.... Shakespeare, of course.... Horace and Seneca.... Yea, in the palaces of Tutankhamen was our work done.... Scraped on rock, in many a primordial cave, are certain drawings. And there are those among us who believe that these were left by the earliest members of the Brotherhood. But this is only legend..."
The Priory of Sion in The Da Vinci Code turned out to be this at the end of the day. All the organization is concerned with is protecting the descendants of Jesus and practicing their own brand of Gnosticism. The organization appeared to be an Ancient Conspiracy and much more powerful at first glance because it attracted a lot of bright people to join its ranks; however, the achievements of these members (that we know of) are almost always accomplished independently of their Priory membership.
Although how much they aid the protagonists is debatable. Giles might be a good guy, but most of the time, when the other Watchers show up, they actually cause problems for the heroes.
The Illuminati in the first Deus Ex sort of fall under this trope in the first game, as they would originally, at least according to Everett, only "influence" the world, instead of directly controlling it. They help you in the fight against MJ12, but it is questionable if their motives are any better, especially when you see that Everett has one former leader in semi-cyro to keep him alive and conscious for advice, while falsely telling him that he cannot cure his illness. The second game on the other hand, they are definitely not just in the shadows, "influencing".
Deus Ex: Human Revolution reveals that not only do they attempt to control the world (though they're not very successful at it) but they may not even be that "Ancient".
In Scarlet Weather Rhapsody, she's a playable character.
In Subterranean Animism, her power is amongst Reimu's attack mode. She sponsors Reimu to stop Yasaka Kanako'snuclear conspiracy. Kanako herself is two-woman Ancient Tradition with Suwako.
All in all, Yukari has been intervening many times to ensure that Gensokyo is a haven for the youkai. Sometimes directly, usually through proxies.
Somewhere between the types, but more 2 than 1, we have the Archaic in Penumbra, a secret society devoted to researching Aliens and Monsters and keeping them separate from humanity. Unusually for this trope, they're extremely corrupt, and willing to sacrifice the lives of lower-ranking members to protect the upper echelons.
The Treewalkers in The Night Of The Rabbit, who have the power of using trees to travel across different worlds, times and possibilities. They use their magical powers to help the people of worlds they visit.
In ThunderCats (2011), Thundera's Clerics, in addition to acting as Church MilitantPraetorian Guard, also have a more passive tradition of guarding Thundera's history, and keeping the Book Of Omens' contents and location a secret. They allow the book's existence to become mythologized and doubted, and conceal specifics from their ruler, and the people he sends in search of the book. But when an ancient enemy attacks, and the book becomes necessary to defeat him, the remaining Clerics immediately begin providing aid and information to their king.
Santa Claus. The Western tradition of lying about a fictional person giving gifts to children is actually impressively wide spread and frightening accepted as both a matter of course without much thought or organized pre-meditation beyond trying to decide what present "Santa" gives.