All Your Base Are Belong to Us: Loki briefly sets up shop in the Avengers mansion for his confrontation with Thor at the conclusion of his plan (see Darkest Hour below), before moving on and occupying the royal palace.
Arch-Enemy: Thor and Loki, as per the mythology and comic canon.
Oddly subverted, however, with Trixie and Twilight Sparkle — Trixie describes Twilight as her "nemesis" at one point, but after that it's never mentioned again. Heck, the two don't even interact at all in the story (aided greatly by Twilight barely even being in the story).
Also subverted with the Dark Avengers; they each apparently view themselves as the archenemies of their Avenger counterparts, but aside from the Thor/Loki fight, the Final Battle doesn't involve any of the counterparts pairing off (which was the Avengers' plan).
Arson, Murder, and Jaywalking: Pinkie steals Mjolnir from Big Mac in order to get him alone and talk to him about it. Afterwards, she apologizes for it:
"I'm sorry I followed you home and broke into your house and stole your stuff and ate the last of your pancakes-"
And then she does it again when she breaks into Spitfire's apartment to talk with her:
"Sorry about sneaking into your room and waking you up and scaring you and eating your last pie..."
Bastard Understudy: When it seems as though the villains have won, Trixie tries to betray Loki. Unfortunately for her, he was prepared for that.
Chekhov's Gun: At first, it seems the reveal that Loki is Pinkie's many-times-great grandfather is just a convenient way for Pinkie to know everything about Thor. Then it turns out that that blood link has been allowing Loki to spy on Thor's every move.
The Chessmaster: It turns out Loki (who actually makes a chess metaphor at one point) manipulated pretty much everything in the story up until the climax to insure his victory and it temporarily works. Big Mac managing to outsmart him just prior to the Final Battle actually contributes to his Villainous Breakdown.
Both Avengers vs Dark Avengers fights — the first was this for the bad guys, the second was for the heroes.
Darkest Hour: Chapter 14 — Loki's Dark Avengers have defeated the Avengers, and a threat on Pinkie's life gets Big Mac to surrender Mjolnir and Thor's power; Loki then perverts The Power of Friendship in order to steal the other Avengers' powers, leaving him unopposed to take over Equestria. Fortunately, the chapter ends with the below mentioned Rousing Speech, giving things a glimmer of hope, and by the next chapter things are already getting better.
Demoted to Extra / Out of Focus: The Mane Six, despite being the heroes in canon — having saved the world themselves twice — have almost nothing to do with the plot here. Pinkie and Rarity are secondary characters at best, only due to their relationships with two of the main characters; Applejack shows up even less, despite being the main character's sister; Rainbow Dash and Twilight Sparkle only show up in a handful of scenes; and poor Fluttershy only shows up in one scene and doesn't even have any lines!
Determinator: Much like his comic book counterpart, Caramel is this even before he becomes Captain Equestria (and is actually the main reason he was chosen for the project). This shines through the most during his fight with the Ghost Flyer, where he overcomes the Penance Stare through sheer willpower.
The Dragon: Trixie is Loki's only real servant for awhile, and even after the Dark Avengers show up, she's still his most powerful minion.
Dragon Ascendant: After Loki's defeat, the last scene shows Trixie effectively becoming the MLP version of Doctor Doom and swearing revenge.
Epiphany Therapy: Near the end, Big Mac fully comes into his role when he realizes that he and Thor were never truly separate beings. One of the benefits of this, besides peace of mind, is that Big Mac can turn into "Thor" without holding onto Mjolnir.
Evil Sounds Deep: Implied with the Ghost Flyer — all of his dialogue is capitalized, and the first letter of each sentence is also in bold.
Fire-Forged Friends: Played with with the Avengers. Despite an initial fight brought on by a misunderstanding, they all get along pretty well — but it's working as a team where they have trouble. It isn't until the fight with the Juggernaut that they learn to work together. After that, they're True Companions.
For the Evulz: Seems to be the Red Skull's primary motivation. While the other villains are after power and/or revenge, the only reason he gives for his actions is his belief in his natural superiority, but even that across as a pretty weak excuse.
There's also Gilda when she becomes the Juggernaut, but she was being manipulated (and possibly indirectly controlled) by Trixie and Loki, so she may not really count.
Fun Size: Celestia gets shrunk down to a filly after Loki attacks her and drains a good portion of her power.
Götterdämmerung: A critical part of the backstory — Loki's attempt to overthrow Odin and take control of Asgard led to its destruction and the death of all the old gods (excluding Loki himself), the magic released from this creating Celestia and Luna in the process.
Green Thumb: Caramel gains this ability in addition to super strength when he becomes Captain Equestria, due to his natural Earth pony abilities being amplified.
Kick the Dog: As if them threatening to kill Pinkie in order to get Thor to surrender didn't already qualify, the fact that Loki and Trixie threaten to do it slowly certainly does, if not verging on Moral Event Horizon.
Lampshade Hanging: Several characters point out how much this situation is like something out of a comic book.
Large Ham: Thor, Loki, Trixie and Luna all in one fanfic? The author included a warning tag, but with that character gallery, it shouldn't have been necessary.
Manipulative Bastard: Loki. And arguably Trixie, but she was just doing what Loki told her, rather than manipulating people herself.
Mass Super-Empowering Event: The destruction of Asgard ages ago is apparently what gave ponies the magic they have in canon and created Luna and Celestia. There's a second one early on when Celestia is attacked and forced to release her magic, giving random superpowers to those nearby. And a third when Loki is finally defeated. According to Loki the combination of all three will ensure that everypony (and every other speices) will be mutants within a few generations.
More than Mind Control: Something else the Wrecker and the Juggernaut have in common — they're both granted their powers by Loki (via Trixie) and do what they want with them, but are guided by a subliminal hatred of Thor (and the Avengers as a whole, in the Juggernaut's case).
Ms. Exposition: Pinkie is the one who explains the origins of Thor's powers and rivalry with Loki to Big Mac. As it turns out, she knows all this because she's Loki's many-times-great granddaughter.
Mythology Gag: During the epilogue, Twilight (now the Sorcerer Supreme) is shown sealing away the demon Tirak, the antagonist from the G1 movie "Rescue at Midnight Castle".
Near Villain Victory: Loki succeeds in defeating the Avengers, stealing Thor's power, and usurping the throne of Equestria. In the end, he is only narrowly defeated by a last desperate plan the Avengers put together.
Nice Hat: Subverted. Big Mac refuses to wear Thor's helmet, because he thinks it looks ridiculous.
No Fourth Wall: Pinkie naturally. Does it offscreen to bring in Stan Lee as a pony! It's a nice little tribute.
Odd Friendship: Big Mac and Pinkie strike one up, based on Pinkie being Ms. Exposition. It gets to the point that Applejack assumes they're dating (to their amusement).
OOC Is Serious Business: You know Rainbow Dash has become a Thor fangirl when she's so excited about attending a party in his honor that she forgets the Wonderbolts are going to be there too. Pinkie and Big Mac are left rather stunned.
Revenge: The primary motivator for many of the villains — Trixie seems to want revenge on the world in general for not giving her the praise she thinks she deserves, the Ghost Flyer and Iron Monger want revenge against Spitfire and Blueblood (respectively) for perceived slights, and even the Wrecker's brief career is based on revenge against Rainbow Dash for upstaging him.
Rousing Speech: Big Mac gets one from a ponified Stan Lee, of all people, during the Darkest Hour. He then proceeds to give one to each of his teammates, pulling the team back together.
Sequel Hook: The epilogue shows the ponies adjusting to the new world, and Trixie plotting her revenge.
Shared Universe: In the commentary for the epilogue, the author not only announces his attention to (eventually) write a sequel, but also welcomes anyone else to make additions to what he calls "Marevel Equestria" (so long as they don't use the Mane Six or Thor's team without his permission). Onlyrecently has anyone started taking him up on the offer.
Ship Tease: When the Princesses first meet Thor, Luna appears to develop a crush on him, though it never comes up again. Likewise, Celestia flirts with him, though that seems to be more to troll Luna than anything else.
Shout Out: When Pinkie is first explaining Thor's backstory to Big Mac, she starts by giving him the basic information with what appears to be a psychic headbutt.
During the epilogue, when Twilight is sealing away Tirek, she does so with the "Chains of Mag'ne".
"THOU ART THE ONE WHO KILLED THE GODS THEMSELVES! THOU DESTROYED OUR HOME AND OUR FAMILY! THOU HAST CAPTURED THE SOVEREIGNS OF THIS LAND, USURPED THEIR POWER, AND THREATENED ITS INHABITANTS, AND YOU DARE ACCUSE ME OF DEFIANCE?”
Smug Snake: Loki and Trixie (the latter even moreso).
Split Personality Takeover: Big Mac spends most of the story worried that Thor will take over his mind. Near the end, he realizes he was being silly when he finally accepts that there was never really another person inside him — he may have Thor's memories and powers, but he's still Big Mac.
Unwitting Pawn: The Wrecker and the Juggernaut, who were granted their powers by Loki simply as a way to lure Thor out of hiding (the former) and to test the newly-formed Avengers (the latter). And then it turns out that Loki was stringing everyone along in order to create a scenario wherein Big Mac would willingly surrender Thor's power to Loki.
Villainous Breakdown: Loki loses it in the Final Battle thanks to the triple whammy of Big Mac becoming Thor again, the Dark Avengers being defeated, and the revelation that the "Thor" he was fighting wasn't really the brother he considered a Worthy Opponent but a 'mere' farm pony tapping into Thor's power.
The Dark Avengers have minor ones of their own — the Ghost Flyer's is of the "This Cannot Be!"-inspired panic variety when Captain Equestria breaks through his Penance Stare, while the Iron Monger and the Red Skull go into blind rages following Firebird and Iron Pony's respective Shut Up, Hannibal! and "World of Cardboard" Speech.
Visionary Villain: At times, Loki seems to want power merely for the sake of power, but really, he has a vision of a world ruled by magic (preferably with him as ruler), and seems to think it would be for the best. He therefore dies happy, knowing that his death will ensure everyone gains powers, thus creating his world of magic.
Walking Wasteland: The Red Skull drains the energy from living things, so plants have a tendency to whither around him.
Wham Episode: Chapter 13, in which the Dark Avengers first appear and defeat the Avengers, followed by chapter 14, wherein Loki reveals his Gambit Roulette and forces Big Mac to surrender Thor's power.
"Where Are They Now?" Epilogue: Closes up the story, incorporating the later adventures of not only the central characters of this story but also Twilight Sparkle as Sorcerer Supreme and Rainbow Dash as Quicksilver, leader of an action team featuring ponies with X-Men powers and codenames.