Kenneth Miller's book Finding Darwin's God uses this as part of its demonstration that acceptance of evolution does not actually have to have any effect on one's belief in God, as a deity who can create life through manipulation of natural laws would have a greater claim to omniscience than one who could create life from dust. Deals primarily with Christianity (after all, who else is having the running battle with Darwin?) and makes excellent points about how a truly omnipotent, omniscient God working in evolution is not only more impressive than the "boom, stuff happened" God, but also completely compatible with Christianity.
This is usually pulled as the explanation for God in The Dresden Files. This trope is invoked on several occasions, usually by Knights of the Cross. Harry usually does not take this as an acceptable answer.
Lampshaded in one of the later books, with Harry basically asking someone "They tried the "mysterious ways" line on you too, huh?"
In the novel Small Favor and the short story "The Warrior", the archangel Uriel deconstructs Harry's criticisms of the "mysterious ways" explanation, illustrating how through apparently random, unconnected events God had used Harry to change many people's lives for the better without him even being aware of it. Uriel further points out that it only seems mysterious to Harry because God is omnipresent and omniscient, operating everywhere, at all times. What seems incomprehensible to a mortal's point of view, rooted in a single space and time, is not nearly so to God.
Also parodied in one of the books. When Murphy contemplates, how can the garden of the Carpenters be still green so late in the autumn, Harry answers: "Sod works in mysterious ways."
The Eternals in Isaac Asimov's The End of Eternity work like this; at the very start of the novel, the protagonist changes the course of history by moving one particular item to a different shelf. It turns out they work this out with a particular branch of mathematics.
In the short story "Spell My Name With an S", two angels, on a bet, manage to completely avert nuclear war just by convincing one man to spell his name with an S instead of a Z.
At the end of Good Omens, Crowley points out to Aziraphael that an omniscient, omnipotent god would never have allowed them to prevent the apocalypse, or for that matter have allowed Lucifer's rebellion unless that was what He wanted all along. He goes on to suggest that the war between Heaven and Hell isn't so much a chess game as an incomprehensibly complex game of solitaire.
Near the beginning of the book it is said that God does not play dice with the universe, He plays an ineffable game of His own devising which might be described from the vantage of the other players, i.e. everybody, as 'playing a complex and unintuitive version of poker in a pitch black room with blank cards for infinite stakes, with a dealer who won't tell you the rules and who smiles all the time ' (paraphrased).
There was no god involved, but in The Science of Discworld III: Darwin's Watch Hex claims that the voyage of the Beagle was almost as significant an event as Joshua Goddelson leaving his house by the back door in 1734, leading to commercial nuclear fusion being perfected 283 years later.
In To Say Nothing of the Dog, no divinity is ever mentioned, but this is the way the universe corrects potential errors due to time travel.
In All Clear, a theory is presented that the universe regarded the Germans winning World War II as such an error, and has since corrected it via time travel through amazingly subtle coincidences without anyone realizing it.
In Robin Hobb's The Soldier Son trilogy, the Speck magic, as well as Orandula the god of balances manipulate the protagonist through a series of convoluted chains of events, most of them set off by tiny, seemingly insignificant actions, like giving a stone to Caulder Stiet, which leads to the discovery of gold in the plains, which leads to almost all Gernian troops being pulled from the Specks' land, thus protecting the Ancestor Trees from being cut.
Kurt Vonnegut's novel Cat's Cradle introduces the religion of "Bokononism," wherein all living beings are arranged by God in groups called karass, in order to advance the divine will. The members of a karass may never even know each other, and their work may overlap in bizarre, coincidental ways, but they work together for a single purpose that they'll never know.
Of course Bokononism admits that it's all bull shit.
It's implied throughout J. R. R. Tolkien's work that Eru (AKA God) has his hand in everything. Gandalf in The Lord of the Rings explicitly states that "Bilbo was meant to find the Ring, and not by its maker."
Falling Sideways has a plot consisting more or less entirely of the main character being jerked around, tricked, told lies, arrested, told more, contradictory lies, framed, abducted by aliens, told yet more lies and finally being given most of British Columbia, thanks to the plans of a godlike figure whose real motives are an absolute headache to work out and who seems to suffer from major Complexity Addiction. Discussed around the third or fourth set of elaborate falsehoods, with the protagonist cracking that all of the moving in mysterious ways is clearly God ducking to avoid the things being thrown at Him.
God's interactions with Joan on Joan of Arcadia. God will tell Joan to do something, for reasons that aren't immediately apparent, but which makes sense by the end of the episode. For example, in the pilot, God tells Joan to take a job at a bookstore. After coming home from work one night, Joan runs into a man who she thinks is God in another avatar, but who's actually the serial killer her dad's been following. Joan figures this out and escapes from his car, causing him to crash, which causes the police to find him and arrest him. It also motivated Joan's brother to get out of the house and get a job.
God: I work in mysterious ways. So do you.
Similarly (to the point that FOX tried to kill the series so no one would accuse them of ripping off Joan), the talking toys in Wonderfalls. Each will repeat a short phrase to Jaye, who has to act on what little evidence she has for a generally beneficial result (or else they will harass the shit out of her). One episode has a toy penguin tell Jaye, "Bring him back to her!"; after some desperate flailing, Jaye manages to a) restore a nun's faith in God, and b) reunite a priest with his wife and daughter. In some episodes, Jaye deliberately decides not to follow the advice of the toy animals, which still results in everything working out right.
Quantum Leap. At one point, Al theorizes that "God, time, fate, whatever" is responsible for Sam's leaps, as something is obviously helping Sam leap into people who need help. In the series finale, Sam meets that "something" in the form of a bartender. The bartender points out that, contrary to what Sam believed, his leaping has had a significant impact on the world. Sam may have only helped one life at a time, but those lives touched others, and those others. The bartender congratulates Sam, telling him that he has done a lot of good. This convinces Sam to continue leaping instead of trying to get back home.
In Supernatural, where God's presence is zero for the first three seasons. Then in season 4, He sends an angel to revive Dean from Hell and starts being a lot more proactive. When Dean questions Castiel about it, Castiel begins to state this trope, but Dean cuts him off and warns him, "If you say 'In Mysterious Ways,' so help me I will kick your ass." A later episode shows that God's ways are so mysterious, even Castiel doesn't know what's going on.
The archangels, and Lucifer, all seem very certain their father is real, but that he is either dead or just gone forever. As one might imagine this distresses them. Castiel wants to find him and ask what's up.
They found out from an angel named Joshua that God is on Earth and aware of Apocalypse, but simply doesn't care. Cue to severe despair for Dean and tremendous lost of faith and start of severe alchoholic problems for Castiel in following episodes.
Later it is implied that Chuck, the prophet who began writing Dean and Sam's adventures for profit, might have been God the whole time and was slightly guiding them. Of course, considering some hints from Gabriel, Lucifer and others and the way all angels and humans are, it still doesn't excuse him of being one hell of a lousy father, considering Gabriel decided to ditch them and turn into the Trickster, Lucifer... well, you know the rest. In retrospect, this means that when Chuck was apologizing for making them live bad writing, he was apologizing for their entire lives.
In a later episode (Reading is fundamental) Castiel outright invokes this trope by reacting to Dean's question on what kind of sense some angelic plan makes with "That's god and his shiny red apples."
In Saving Grace, God's plans for protagonist Grace Hanadarko, the nature of angels or the reasons for giving her a shot at redemption, thus often investigated in many ways, will stay mysterious to her until the very last episode.
The qashmallim of Promethean: The Created, "angels" made of the Divine Fire that gives Prometheans life. They manifest for only a short while, and have one particular purpose they must complete in that time. This purpose can range from bringing two people together to causing a nuclear meltdown, all in service of "the Principle."
It's been revealed that the upcoming God-Machine Chronicle and Demon: the Descent place angels, the agents of the God-Machine, in a similar role. Word of God casts them as more similar to the Observers on Fringe or the Strangers in Dark City, agents of the great machine aiming to keep the machinery working. Strangely enough, sometimes the God-Machine will set two angels at cross purposes, then make both of them fall when neither truly achieves their goal.
In Nomine is interesting in this regard: If you roll a 111 or 666 on a 3d6 roll, either God (on a 111) or Satan (on a 666) intervene. What this means depends on which side of the War you're on, but the GM is encouraged to work in this method (for example, a Demon doing something explicitly supernatural, on a 111, will discover a warrior Angel-for reasons of his own- walking around the corner right as the Disturbance is traceable to him).
Tzeentch, Chaos god of change, Chessmasters, mutation, Chronic Backstabbing Disorder, magic and embodiment of all hope in Warhammer and Warhammer 40,000 is very much this (though with considerable competition from Cegorach the Eldar Laughing God, the C'tan Deceiver, and the God Emperor of Mankind). His entire reason for being is to make stupidly-complex Xanatos Gambits that span millenia, and everything that makes one of those plots fail merely ensures that it causes another to succeed. Which is why the unofficial Catch Phrase of his Sorcerers is "Just as Planned" in response to anything happening.
Ciaphas Cain (HERO OF THE IMPERIUM) considers the God Emperor to be this, remarking several times that his life could have turned out radically different, but the Emperor works in mysterious ways/has a twisted sense of humor.
"We must simply accept that God can change without explanation, just as we accept that first Dick York was Darrin and then suddenly Dick Sargent was Darrin."
This is the title of the opening number of the musicalThe Color Purple, celebrating God's power to bring good out of evil. However, there's powerful potential for Alternate Song Interpretation there - here's this church full of Gossipy Hens speculating on the life inside the home of a man whom they know is abusive, yet they don't lift a finger to remove his two daughters (one of whom is pregnant for the second time, and fourteen) from his house.
Parodied in Fable III. After completing one sidequest, the villager you helped exclaims that the gods must have sent you to help him out. He then starts to examine this idea more deeply and reasons that it would be logically inconsistent to credit good things to divine will whilst at the same time writing off the bad as mere misfortune. Hence, not only was you saving him all part of the plan, but so was him getting into trouble in the first place, the stress he went through, and every minor problem he's ever faced. He ends up desparing at a Universe that is at best indifferent to human suffering and at worst actively malicious.
One of the Strangers in Red Dead Redemption can be found lying in the desert, delirious and sick. The first time you offer to help her, she sends you away saying God will save her. If you come back to give her medical supplies, she decides that obviously she was right, because God sent you to help her.
Parodied on American Dad! when Stan meets God after learning his family is about to die.
God: Everything happens for a reason. Stan: What reason could there be? God: Stan, I'm gonna level with you. If your family is allowed to live, Stanford's tennis team will go 0-and-8 in conference play.
The closest thing Futurama seems to have to God, a sentient nebula, believes that this is the way Godshould behave. Unlike many examples, it actually explains why it believes this way: If a deity does too much for its people, they will become dependent on it; if it does too little, then its people will not be able to deal with problems beyond their abilities. By working in mysterious ways the people are motivated to work hard and expand their knowledge, but can still receive help if they need it.
When you do things right, people won't be sure you've done anything at all.
It was also a stark contrast to how Bender played God to some tiny sapient beings living on him. By asking them to do him favors, it ultimately introduced crime, while maiming and killing hundreds, if not thousands. By trying to help, he killed scores of them and destroyed many of their crops. By doing nothing, those he hadn't paid attention to felt ignored and eventually waged all out war that resulted in mutually assured destruction, using weapons built from Bender himself. Speaking with the nebula changes Bender, and goes out of his way to rescue trapped monks. It is then revealed that, because this action was done of Bender's own will, but only because of the nebula's influence, the nebula saved the monks, though they will not credit him, thus showing his philosophy in action.
One of the most common interpretations of Princess Celestia from My Little Pony: Friendship Is Magic; despite doing seemingly very little, she seems to always have things set-up to turn out alright…even if such plans had to be so convoluted and unlikely to barely be noticeable at all. For example, is the only reason she was so calm about Nightmare Moon's return because she's somehow known (or arranged for) all the potential Elements of Harmony to be in Ponyville at the correct time?
On the flip side of things, He might let some miserable/unfair/despair-worthy things (minor and major) happen to both good & bad people because it will give them the opportunity to learn and grow more than they ever could have in more comfortable situations, as many people who have had troubling pasts can attest to, if they admit that they wouldn't want to go through whatever had happened to them again, but at the same time they wouldn't want to take those experiences away, because those things shaped them into the person that they are today. Whether somebody gains or learns something from a bad experience is ultimately up to them, though.