Blood and Honor: "There is no death, there is the Force." Sanguis hears this phrase from rebel Sith Kel'eth Ur early in the story, then finds them repeated to her by various Jedi she encounters. She struggles to understand what it means, since, as she's lost both her mother and her mentor, death seems very real and permanent. Not until the end of the story does she realize how the Force connects all life, which helps her see the underlying meaning of the words.
Child of the Storm has variations on "a storm is coming" throughout Book I, alluding to the constant, steady build-up of trouble and evil, before the storm is finally unleashed in the epic 4 part finale (chapters 75-78, not counting the two chapter epilogue. An argument can be made for chapter 74 being a part of it too), when everything comes to a head. It relates to the title, with Harry being the titular 'Child of the Storm.' As the son of Thor, this is literally true, but with the way trouble tends to follow him around, and how he's at the very centre of events (by the design of Doctor Strange), it also refers to the more figurative storm.
Doctor Strange's Catchphrase, "Check," pops up a couple of times before the finale, alluding to his nature as The Chessmaster who's been manoeuvring everyone, with his final, understated Badass Boast being "Check. Check and Mate."
And then there are the repeated references to how Harry can either be a bright and shining Messianic Archetype or a terrifying Dark Messiah based on his choices.
Kirby's Dream Cafe has We Stay. They represent Kirby's coffee shop desire to stay. They appear at least once every chapter except the prologue (which set up from what they were staying) and the 4th chapter, where they left at the end to get Kirby to a hospital.
The Party Never Ended has a unique example, in that the arc words are heard by the main character, but are not actually revealed to the reader until near the end. Every time the arc words are brought up, they get their own arc words: "It said seven simple words to her..." The true arc words are "I love you, Pinkie! Please wake up!"
Pipeline has this one: "Sometimes being strong isn't enough. Being brave, and good, and determined isn't enough. Sometimes things just happen." Kevin says it to Blossom and Bubbles after Buttercup dies, and Blossom repeats it back to him at the end of the fic when it looks like Ben might not pull through. Even though Kevin says it himself, he doesn't really get it until later.
Almost all the stories end with the pony in question accepting her new position, declaring "I'm free." In the Discorded Series, this is normally a bad thing, but in the Reharmonized Series, it's a good one.
"Pearls" for anything involving Fluttershy and Fluttercruel.
There's an arc SONG in the form of the three "So Many Wonders" reprises: The first is about Fluttercruel's happiness over being free from Fluttershy and able to see the world, second is a Villain Song by Princess Gaia used to hypnotise ponies into her vision of the world, and the final is a Triumphant Reprise at the finale of the arc, Fluttershy and Fluttercruel singing together about how their worldview has changed for the better.
"Dying is easy, living is hard" for the entire series, but especially the Dark World. While in the main series it deals with overcoming what Discord did to them, in the Dark World it's about living with what you've done and the world you live in.
"Forgiveness is not earned, it's given" for the Dark World. In addition to the above theme, Forgiveness is an overarching theme, both being able to give it and being able to accept it.
Horseshoes and Hand Grenades: "Death is never the answer." This quote is based on how Ryusei's decision to kill Gentaro caused the events in the story to rise, and how things could've been settled differently other than by killing others. Most notably, this only works for Horseshoes only, as Wheel of Fortune has Mei wanting her parents and the jerkwad people who were 'posing' as her friends dead.
The Swahili phrase "Kufa inadwadia" is this in Series Three. It translates to "Death is coming", foreshadowing the arrival of Death — the Big Bad of that series — in the finale.
"Kill or be killed" is this for Series Five. Survival is a common theme in the final series, leading to many character deaths.
In The Legend of Total Drama Island, the chapter-opening boilerplate periodically mentions in passing that Brett's mother has "neither spouse nor partner". For most of the story, this appears to be merely a narrative flourish. Appears to be.
A Growing Affection has "Rank does not equate to skill" as the Arc Words for the first two books. The title also applies, though it is only mentioned once, while "Rank does not equate to skill" appears a few times and in different permutations.
In the Girls und Panzer fanfic, Off The Path, the title is repeated in a few different contexts, usually in the context of the tank falling in the river that Miho saved at the cost of losing the championship, but later in the fic, it's mentioned again when Maho ponders that the incident "should not have been enough to force Miho off the path she had walked until now". The final sentence inverts the phrase, and the latter two uses signify that the fic is not just about the incident, but how it affected Miho's changing approach to tankery.
Miho: Whatever happens, from here on out, I will continue forward in tankery, on the path I have chosen for myself, along with those who have chosen to walk it with me.
In the MLP:FiM fanfic Mother Of Invention: "NEC DI NEC DOMINI" (translation: "neither gods nor masters"). This mysterious inscription has turned up on every structure Applejack finds.
The title of Necessary To Win is used repeatedly, and in various contexts, including what decisions are necessary to win, whether certain people have what is necessary to win, and whether it is necessary to win, or whether victory can be sacrificed if necessary.
The End of Ends: "Things change, Beast Boy. The girl you want me to be is just a memory."
This Bites!: What Cross first said to Smoker as part of his The Reason You Suck speech way back in Loguetown is recycled and refined in Alabasta, and afterwards used by Cross and Smoker himself multiple times to convince other Marines that the World Government is Corrupt and need to be rebuilt from scratch.
"A good Marine follows his orders to the letter and sacrifices everything for the sake of Justice, while a decent Marine sacrifices everything for the sake of all even Justice, if it comes down to it."
"Speak the problem and it will be solved," in The Keys Stand Alone: The Soft World. In fact, the entire world seems to be swimming in Arc Words (labeled Gods Chat by George after he hears that the Pyar gods might be providing them) in graffiti, on message boards, etc, but this particular phrase comes up most frequently, and the four lampshade it on occasion. They do finally discover what the phrase is for (it's how to remove the curse on the Last Wizard) and also that every other piece of Gods Chat is actually a game clue, since they've been in a giant telepathic MMORPG all along.
In the Eye of the Beholder has "Beholder", used to describe Lydia in particular, and present each time she manifests a new Social Link.
Each book of Forum of Thrones has its own arc words. For Book 1, they are the words of House Raylan "We Write History". Book 2 features the words "All For Our Pride", the words of House Reyne of Castamere. Book 3 is planned to feature the words of House Manwoody, which are "No King Above Me".
The fourth and fifth editions have "It always rains", an allusion to the cyclical nature of things, which include the fact that the Final Battles of each story in the first Myth Arc include battles in the rain.
The second myth arc, which runs from the sixth to eighth editions, uses a sort of inversion. In the final entry of both HU6 and HU7, someone comments on the fact that it's not raining, reflecting how this arc is more of a single ongoing story across multiple editions. When it finally does rain at the climax of HU8, it's a sign that this really is the end.
"WMYD?"note "What must you do?" , of course, not to mention the other two Hypnotic Questions: "Who do you obey?" and "How much (do you obey me)?" All three come straight from the original Nimja files on which this fanfic was based.
The answers to the three questions, "obey," "you," and "completely," also count, and when translated into Dutch form what are arguably the trueArc Words of the series: "Ik gehoorzaam u volledig", which is Dutch for "I obey you completely."
A Man of Iron: Book 2, A Crack of Thunder, has the riddle of the king, the rich man, the priest and the sellsword. Every character has a different answer to who dies, which tells a lot about their personalities. Tony says that they're all just symbols, but those symbols have power. The Night's Queen quips that they all die, because no one thought the disregarded whore in the room with them was dangerous. Natasha states none of them truly live, because they've allowed themselves to be trapped in the game of thrones. Doom believes that you can only survive if you take on all three roles. And Magneto, naturally, says the one who lives is the one who doesn't need sellswords to kill for them... right before he slaughters the Bloody Mummers.
Devils Diary has "Resist the Temptation to Bend", constantly repeated by Magneto to remind himself he must be strong and ruthless enough to do whatever it takes to protect his people.