More often than not when a story has a Big Bad there will be a Big Good to counter them. This has a number of advantages; it keeps the heroes' side balanced against the antagonists', provides a source of support for the heroes and generally stops the series getting too cynical. On the other hand, it raises some problems. Namely, with the strength of such a strong ally, where's the tension? The Big Good could easily end up being a Story Breaker Power, which also begs the question of why they don't get off their arse and send their villainous counterpart packing (or vice versa).
Cue this trope - a powerful benefactor of the heroes (essentially doing the same thing in the story that a Big Good would) who has their own agenda or reasons for helping them. Perhaps they're mysterious and hard to trust, perhaps they're visible, but seem a little too keen to Shoot the Dog. Other times, they're genuinely benevolent beings who are working within some sort of non-interference clause, and may employ the same tactics as their opponents. Either way, they'll provide the support the cast needs, but the heroes (or at least the audience) don't quite know if they can be trusted. Even if they are the Big Good proper, they might not be planning to do things in an entirely moral manner or have it in for the heroes and wish to make them suffer more than they really need to. In a worst case scenario, they might become the new Big Bad or turn out to be a Bigger Bad.
Remember that this isn't a simple case of Omniscient Morality License or In Mysterious Ways, nor are they a Big Good who likes to stay hidden or keep an air of mystery around themselves; the entity in question must be at least visibly untrustworthy rather than having an excuse for their seemingly questionable behaviour. A hero with this trope as their main support might (but doesn't always) find themselves as an Unwitting Pawn, although to count as this trope, the Mysterious Backer must further the heroes' agenda as much as their own (assuming they aren't one and the same). They're quite fond of the Passive Rescue (particularly when it means the hero might be forced to do something on his way out).
A subtrope of The Powers That Be and Mysterious Stranger. See Poisonous Friend for another type of ally who might not see eye to eye with the rest of the team. Contrast with Big Bad Friend, for someone who's close to and trusted by the hero, but leads the villains, and Enigmatic Minion for someone who's on the villain's side with unclear motives.
Urahara from Bleach. He guides Ichigo through the whole series, and obviously knows more than just about anyone else when it comes to just what the hell is going on, but don't expect him to fill you in any time soon.
Green Lantern's Guardians of the Universe. They think they're the Big Good, but they're completely full of themselves and wind up being the cause of a lot of messes the Lanterns have to clean up.
As of the New 52, they've given up all pretense of this, attempting to annihilate all life in the universe by converting it into the Third Army.
Invoked in the second series of Runaways. A group of former superheroes get a mysterious phone call asking them to come out of retirement for One Last Job. The heroes call him out, but they still wind up taking the job.
Most of the major Marvel principalities, particularly the Vishanti. They're mainly on the side of good, but they have a perspective which is sometimes completely alien to normal humans. On more than one occasion Doctor Strange has renounced them, taking the loss of power as a consequence, rather than be beholden to them any longer.
In the Star Wars prequel trilogy Senator Palpatine fulfills this role, since he's apparently helping the protagonists, but anyone who had already seen the original trilogy knew what he had in mind.
In the film Upldr, Lucius appeared to Victor to offer him funds, technology, and even a brain.
The Ellimist from Animorphs technically tries to help the heroes, but he is either too roundabout in his methods to really gain their trust or too held up by Crayak (with whom he has a self-enforced stalemate) to help at all.
The Vorlons were this in the first part of Babylon 5. Their definition of good (as opposed to the chaos of the Shadows) lets them help the heroes, but they go past good. Soon they are blowing stuff up veering into Lawful stupid territory.
Escher and his Piron Corp. from Continuum. Escher obviously has motives of his own, but he does help Kiera out every once in a while despite her open contempt for him, not to mention that in season 2 he begins funding the police department, which the public ends up (rightfully) accusing them of having a conflict of interest because of it, although it still obviously helps with the department's resources.
Definitely an odd example, but the "Machine" from Person of Interest. It's a practically omniscient computer that can see and hear almost everything happening in the entire country, and while it does provide the "team" with the basic information they neednote The Social Security numbers of either the victims or the perpetrators of a violent crime being plotted (which is called the "irrelevant" list), and nothing more to carry out their "mission", it never, say, leads them to catching their (and arguably the public's) biggest threats, i.e. the various Big Bads they face, unless they happen to line up directly with the Machine's "Irrelevant" list.
While it's true that the Machine's creator, Finch, intended for it to be as inaccessible to everybody as possible, and to not give out information that anybody could use personally so as to keep anybody (himself included) from abusing its power, and it hasn't ever lead them directly to a Big Bad, even when violent crimes are plotted and happen only because of them. It only gives Finch their numbers if they're personally involved in the violent crime, even though it must know that some of these numbers have, and will continue happening only thanks to the people who are masterminding them.
It's also been shown to be perfectly capable of giving out reliable on-the-go information, although, granted, this only happens in certain specific situations (after Finch made it personal-use proof), such as when something is happening to the Machine itself, like while it's searching for a new administrator after being attacked by a virus, following a self-reboot.
Definitely some bonus points for it, at times, learning. It's even occasionally been vaguely hinted at being self-aware.
...Which ended up practically stated as true in the episode Aletheia.
There are also some other things even Finch couldn't predict and doesn't completely understand about it.
Of course, this is also what Finch is to John, from John's point of view.
The villainous hacker Root has a Heel-Faith Turn when she is confronted by all that the Machine has accomplished and starts treating the Machine as her god. As part of her belief system she does not question the many mysterious things the Machine has her do but takes it as a matter of faith that the Machine has an excellent reason for it. She follows the Machine's instructions without question and is rewarded for that faith when the Machine helps her accomplish seemingly impossible tasks.
Mantarok from Eternal Darkness. Sure it's the only one of the ancients who isn't planning to enter the world and run amok, is activally opposing the others and even spent some time serving as a small village's personal fertility god. On the other hand, it's hardly in a position to oppose humanity and after masterminding the destruction of the other three ancients, who knows what it's planning...
Word of God also states that another ancient is responsible for protecting humans by cleaning away the remains of Eldritch Abominations (as seen in the form of the yellow glow that accompanies the disappearing dead enemies), and may be an example of this (its yellow element certainly blocks Alex's progress in the final chapter).
Sammael from Dark Siders; An archdemon from hell so Powerful that the destroyer had him imprisoned and reduced to an extra. But He uses what power he does have left to help War, the games protagonist, so that War will help him get his powers back (and because he respects a man bent on revenge).
Guild Wars: The Order of Whispers, in Nightfall, is the Big Good organization confronting Abaddon. However, they're a very mysterious lot, none more so than the Master of Whispers himself (one of the NPC heroes the player can acquire during the campaign), and the player character lampshades this in in-game dialogue with the Order of Whispers shrine attendants from which he/she gets bonuses in explorable areas, saying, in almost as many words, "I don't trust you or your Order, but we have a common enemy, so I'll help you."
Theresa in Fable II is textbook this trope — apparently the Big Good of the whole game until the last ten seconds of the final cutscene.
In the Half-Life series we have — say it with me now — the G-Man. Is he on your side? Seems to be, but it's hard to say, and he has a far more sinister vibe than any other person Gordon meets. And he doesn't give you much reason to trust him, seeing as he blackmails Gordon into working for him, puts him in a twenty-year nap without warning him beforehand, sets him down in a dystopian future so he can risk his life sparking a revolution, then tries to kidnap him again — while ostensibly leaving beloved sidekick Alyx Vance to get blown up in a reactor explosion. All very politely, of course. It certainly doesn't bode well for his trustworthiness that the vortigaunts, an unmistakeable ally, stop him from carrying out whatever plan he had for Gordon in Episode One, and are implied to actively prevent him from consorting with Gordon for the entire rest of the game. Not to mention that in Opposing Force, after Adrian deactivates a nuclear bomb that was set to blow the Black Mesa Facility, the G-Man turns it back on and lets the facility blow up, killing what was probably hundreds of people still left inside. However...at the end of the day, he does seem to want Gordon — and the Resistance — to succeed. He just uses questionable means to achieve his goals.
In Mass Effect 2, despite the nature of the organization, Cerberus acts like this towards Shepard.
Zeno Clash has Golem; a mysterious giant with a face that's shrouded in shadow and an extremely out of place Rubix cube in his possession;
When he appears in the first game, he seems to know exactly what's going on, is opposing Father-Mother and guide's Ghat...but seriously, what the hell are his goals? Plus another Golem was watching what he was doing from afar.
In Zeno Clash 2, Golem's basically become ruler and tried to bring law and order to the land...which puts him at odds with Ghat. This is further complicated by another Golem, who helps Ghat along on his journey (apparently just to see what would happen). To cut a long story short; the first golem's a Well-Intentioned Extremist (who performs a Heroic Sacrifice to set things right), while the second one just likes putting people through cruel "tests" for the sake of it.
In Final Fantasy Tactics, Delita effectively acts as one for Ramza. Delita's biggest contribution for Ramza's cause is effectively deploying Thunder God Cid to fight along his side. Talk about friends in high places...
The composer (AKA Joshua) in The World Ends with You. He more or less manipulated Neku into stopping the Big Bad's Evil Plan and was even considering destroying everything anyway (although Neku's actions made him change his mind).
Metal Gear Solid 2: Sons of Liberty has in its post-credits scene Otacon informing Snake that one of their biggest contributors was in fact one of the supposed members of th Wisemen's Committee, although he shortly thereafter reveals that they were dead since a century before the events of the game.
In the tie-in comic for Batman: Arkham Asylum, The Road to Arkham, Batman suspects that the anonymous tips about Zsasz's activities, Scarecrow's activities, and the location of The Joker were given by the same person. Evidence from the game itself as well as its sequel, Batman: Arkham City, implies that the source of the anonymous tips were either Quincy Sharp, Dr. Strange, or Ra's al Ghul.
Red vs. Blue has the enigmatic Director, head of Project Freelancer.
Vic too in the early episodes, in the sense of being Mission Control with some sort of agenda.
Worm has the Undersiders' unknown boss. Eventually revealed to be Coil
Deconstructed in Scooby-Doo! Mystery Incorporated, during the first half of the first season, Mr E has been secretly helping Mystery Inc in some of the mysteries they are solving, but he soon puts them all in real danger for his personal gain. Such as sending one his hired hands to attack them so that he can lure out Prof Pericles.