A God Am I: Thorne's ultimate plan is to use the power of the Letters of Cold Fire to transform himself into a NightmareAlicornstallion and become the tyrant of as much of Equestria as he can hold against Discord, with the hope of ruling the whole world. Thorne temporarily achieves the first part of this goal.
Twilight Sparkle, when she thinks that Thorne's attack has killed Rarity. You get to see why she is known as one of the strongest mages in Equestria. This is even more Bad Ass when one considers that this is pre-Alicorn Twilight!
Princess Celestia, when Thorne tries to presume on her good nature after he has attacked Equestria and murdered ponies. Do not hurt her little ponies! And do not assume that an ancientAlicornrulingPrincess is foolish or weak!
Black Magic: Rowley's spells all inflict harm on someone, even those which help someone else. Consequently, they are useless from the point of view of Twilight Sparkle, and indeed most Equestrian mages.
Blasphemous Boast: On his first night in Ponyville, Thorne responds to an angry challenge by Rainbow Dash by transforming into a 'Nightstallion' much like Nightmare Moon. It's all an illusion. THIS time.
Body Horror: Thorne transforms Spike and the Cutie Mark Crusaders into tortured, mind-controlled monsters modeled vaguely on the Sunny Towners, in the hopes of demoralizing the heroes by forcing them to kill them. Would Hurt a Child, indeed!
Break Them by Talking: Thorne does this on his first night in Ponyville, promising to reveal 'great hidden truths' to an audience of bored and curious ponies. And he does, by airing everypony's dirty secrets in very cruel fashion, climaxing with revealing that as a filly Applejack once asked Nightmare Moon to end the suffering of her grandfather. This causes a temporary Heroic BSOD in poor AJ.
The Cloudcuckoolander Was Right: Why yes, Lyra, humans are real. And you get to meet two of them. Too bad you've been enthralled by the evil one of the pair.
Fantastic Arousal: John accidentally does this to Fluttershy, based on her reaction (partial wing extension, coupled with embarassment) when he scratches her ear. It's not entirely obvious whether this was actually sexual or simply too affectionate for their degree of intimacy as friends (she says that one wouldn't do it to another pony "unless they know you very well.") John apologizes, and Fluttershy doesn't seem too upset.
Faux Affably Evil: Thorne. And Discord. Thorne presents himself politely enough, but it soon becomes obvious that he enjoys degrading and dominating others.
Folk Music: John's main musical genre. His normal profession is wandering the back country, looking for folk songs to record and preserve.
For the Evulz: Thorne claims to want wealth and renown, but (as Twilight Sparkle points out), he could have gotten these things in fair trade for his knowledge and skills. When Twilight wonders why Thorne would do terrible things instead of treating ponies kindly, the more worldly-wise Applejack points out that some beings are just plain evil, saying "For some skunks, it’s just plain fun ta get what they want by hurtin’ somepony else."”
Food Porn: Happens more than once, given John's first-person POV reactions to Earth Pony cooking.
John really loves the meal the Apples feed him on his arrival. This despite the fact that, they being Ponies, their cuisine is of course purely vegetarian, and being Apples almost entirely made of various apple-based products. But then, Sweet Apple Acres in-canon produces the best apples in all of Equestria.
Most of the inhabitants of Sunny Town want to be resurrected, even if this means subjecting innocents to a living death. Failing that, they want to force others to "join their herd" by draining their lives, trapping them in the same fate. They do not grasp that there is no good way they can simply get their lives back.
In contrast, their kin Ruby, whose murder by the Sunny Towners when they were still alive was what originally induced her friend Luna, (who had just become Nightmare Moon to kill and curse them, wants her relatives to accept their fates and pass on to the next world. She could pass on whenever she wished, but prefers to have her horrible murder re-enacted nightly to abandoning her friends. Too Good for This Sinful Earth applies literally in Ruby's case!
Played straight when Twilight Sparkle wonders why Thorne chooses to use his powers for evil when with those powers he could get anything he wanted in trade for his services. Justified in that Twilight is a member of both a species less aggressive than humans and an aristocatic scholar exemplifying the virtues of a culture which emphasizes the value of friendship and mutual toleration.
HilariouslySubverted when Thorne tries to trick Time AbyssPhysical Goddess Princess Celestia into believing that she can trust him, under a combination of this theory and his belief that Good Is Dumb. Celestia lets him reel out enough verbal rope to hang himself, then telekinetically slaps him around before casting him out into the void between worlds.
Good Is Dumb: Thorne seems to believe this, which is a serious error to make when your enemies include a very heroic and cunning human bard and two of the canonically-nicest and smartest ponies in Equestria, namely Twilight Sparkle and Princess Celestia.
Heroic BSOD: Happens twice, almost happens another time.
Applejack, when Thorne reveals to all of Ponyville that as a filly she wished upon Nightmare Moon for her terminally-ill grandfather's death
Spike breaks down into helpless sobbing when he thinks Rarity is dead.
Applejack and Rarity are clearly close to suicide when they believe they will have to kill a transformed Spike and the Cutie Mark Crusaders, including their little sisters Apple Bloom and Sweetie Belle. They just mean to get Thorne first.
Hostage for MacGuffin: Thorne kidnaps Spike and the Cutie Mark Crusaders and threatens to give them to the Sunny Towners unless the heroes give him the Letters of Cold Fire.
Just in Time: Twice, both times starring Princess Celestia as rescuer.
Princess Celestia bursts into the Golden Oak Library just in time to stop a mind-controlled Twilight Sparkle from speaking literally the last two syllables of the spell that would release Discord back into Equestria. As it is, Discord nearly does break loose.
Killed Off for Real: 2 Guardsponies (including Captain Bastion) and 3 Ponyville citizens die in the attack of the Timber Wolves, orchestrated by Thorne. Several more Guardsponies die distracting Thorne so the Mane Six can reach Sunny Town.
Language Barrier: One of John's initial problems is that he can't speak Equestrian, nor can the Equestrians speak English.
Little Miss Badass: Apple Bloom, who in the very first chapter helps John fight off an undead horror. But then she comes from Ponyville's main Badass Family.
Between being the bearer of the Element of Honesty and her strong common sense, Applejack can usually figure out whether you are telling the truth or lying. Even if you're not a pony.
Between his own strong common sense and mystical awareness, John is also quite good at figuring this out. This is one of the ways in which he and Applejack are Not So Different.
The Lost Woods: The Everfree Forest. Between the usual monsters and the Sunny Town undead, it's not a place even John cares to wander — especially at night.
Magic A Is Magic A: One of the reasons Thorne is so dangerous is that he knows kinds of magic rare in Equestria. One of the reasons why John's help is so important is that John knows how to counter Thorne's spells.
How the Mane Six summon John to Equestria, through what is heavily implied to be the My Little Pony musical theme.
As a bard, most of John's magic also works this way.
Man of Wealth and Taste: Thorne, to the point of underestimating those who aren't. This is a serious error when your enemies include a highly-competent rustic human bard and a whole Badass Family of rustic ponies (the Apples).
Mistaken for Spies: Rainbow Dash's first opinion of John. This is a Continuity Nod to her first opinion of Twilight Sparkle in the series opener "Mare in the Moon". Justified, in that John is of the same species as Thorne.
Morality Chain: When she was still alive, Ruby was this for Princess Luna over a thousand years ago, helping to keep her from becoming Nightmare Moon by showing her that there were ponies who loved and appreciated her and her night. Unfortunately for everyone, Ruby's fellow townsfolk murdered her, both dooming themselves and serving as a trigger for Luna's Start of Darkness.
No Honor Among Thieves: Thorne and Discord are each planning to betray the other once the Princesses have been defeated. What's more, they both know that the other knows it too. This bothers neither of them: it's just the way things are between an Evil Sorceror and his insanechaotic patron.
Not So Different: John (a heroic, honorable, intelligent well-educated rural human) and the Apples (who are heroic, honorable, intelligent well-educated rural ponies) find they have a lot in common, and become friends. To a lesser extent, this is true in general of John and the Mane Six though he and Rainbow Dash rub each other the wrong way: they come to see each other as good people, despite their species differences.
Pint-Sized Powerhouse: Spike is grabbed by the jaws of a Timber Wolf (a huge mass of wood animated by a wolf-like spirit) and receives only minor wounds. He then sets it alight by breathing fire down its throat. But then, he is a literal Dragon, complete with armor and breath weapon.
Power Copying: One of Twilight Sparkle's most useful canon abilities in this story, given how often she finds herself aided by or opposing human magic.
Sealed Evil in a Can: Discord, the story implicitly taking place between the Season Two Opener and "Keep Calm And Flutter On"
Sergeant Rock: Captain Bastion. Though he has commissioned rank, he's obviously a tough veteran who has worked his way up through the ranks. This makes his death in Thorne's first attack all the more shocking.
Staking the Loved One: What the Mane Six believe they have to do after Thorne transforms Spike and the Cutie Mark Crusaders into hideous insane monsters.
Starfish Language: Ponies speak by a far more complex version of equine vocalizations and body language. Human voice boxes and bodies are ill-equipped to produce such noises and motions. The same is true for any Ponies trying to speak any human languages. This is one reason Twilight Sparkle needs the translation spell to communicate with John.
Tome of Eldritch Lore: The Letters of Cold Fire, the book cursed to damn the soul of the mage who reads it and force that mage to release Discord. Of course, Thorne hands it to Twilight Sparkle.
Tragic Monsters: Thorne turns Spike and the Cutie Mark Crusaders into hideous mind-controlled monsters, essentially just to torture both them and the Mane Six.
Translation Spell: Twilight Sparkle casts one on John to enable him and the ponies to speak to each other.
Trapped in Another World: John's situation in Equestria. The Mane Six summoned him, but have no idea how to get him back.
Turn Undead: John's music can do this to the Sunny Town revenants. The actual physical Elements when borne by the Elements of Harmony can do this as well. However, if they've just been used and therefore weakened...
Walking Wasteland: The Sunny Town revenants do this to any living things they touch. This is their main attack against ponies, or for that matter any life forms.
White Magic: Most of John's spells do not harm others, though there are a few exceptions.
Would Hurt a Child: Three times in the story, all involving Thorne and twice the denizens of Sunny Town.
Thorne and the Sunny Town undead, as in their original appearance are only too willing to kill Apple Bloom and make her one of them. John shows up just in time to save her.
Later, Thorne threatens to give Spike and the Cutie Mark Crusaders to the Sunny Towners unless the heroes hand over his spellbook.
Finally and most horrifically, Thorne actually transforms Spike and the Cutie Mark Crusaders into tortured, mind-controlled monsters, in the hope that the Mane Six will kill them, in the process shattering the heroes' morale. This plan almost works.