Acceptable Breaks from Reality: Between the intersection of surprisingly emotionally charged storytelling and standard MMO mechanics that completely screw with it, and the fact that both sides of the crossover are rather known for their warped senses of humor, expect to be ready to nod and go along with it a few times a chapter. By the time you get around to the reveal that Celestia and Luna have alts in the Cutie Mark Crusaders guild you'll probably be game to just roll with the loony.
Baleful Polymorph: This has fast become Twilight's favorite spell, or at least her most used.
Beleaguered Assistant: Morning Star. Most of the Royal ponies, who had gone from defenders of the realms to Mr. Exposition / quest givers to Dungeon Crawlers. They are not amused.
Beware the Nice Ones. Rarity is always calm and good-mannered, even in the middle of a battlefield. Then she gets killed by a cultist, getting her mane burned for extra insult. On their next meeting, she forces the cultist to shoot her companion and then mind-controls her out of the window.
Boom Town: Ponyville had become this barely a couple of months after Neltharion.
Brown Note: Rarity has incorporated her infamous whining into her psychic scream power.
Call Back: Rocky from Party Of One became the totem for Pinky Elemental of Earth. He is nicer than his original version too.
Curb-Stomp Battle: Twilight decided to fight Trixie to shut her up. Trixie had actually been adventuring and taking levels while Twilight had passed her time studying archeology. The results were not pretty.
Cutlass Between the Teeth: apart from Equestria-specific drops, most World of Warcraft weapons are designed for humanoid players. Unless they can be strapped to the legs somehow, they have to be wielded with the mouth.
Death Is Cheap: The cheapest, it is based on World of Warcraft after all. In the prologue Deathwing wipes out Ponyville (except Rainbow Dash, who was flying overhead) and Princess Celestia resurrects them all (except Applejack who was rezzed by a passing Dwarf with jumper cables). Later, during one of the first boss battles, Rainbow Dash is killed and almost immediately rezzed by Fluttershy. And in the second to last chapter the entire party is killed
Hidden Depths: Diamond dogs. They are still greedy underground barbarians but apparently they do have their own culture and religion. They are also highly competent in anything involving earthwork or gems.
Weirdly, could also be said for dying. Dash and Pinkie are big PvP'ers and die all the time, and Applejack's warrior trainer specifically warns her ahead of time that as a tank, dying isn't a matter of "if" so much as "how often". When a Total Party Kill happens and everyone's in various degrees of freaking out due to being dead, the three of them take it in mild irritation, embarrassment at having caused the wipe, and admirable stride respectively.
Kill 'em All: The prologue. Deathwing torches most of Ponyville, who then have to be Mass Resurrected by the princesses. (Except for Dash, who was flying too high to be caught in it. She then grouses that she missed the achievement.) Taken lightly at first, but the various flashbacks to the Cataclysm give rather sobering accounts of the fact that, yes, everypony really did get violently burned to death. Worse still, Sweet Apple Acres was outside the Mass Resurrection radius — were it not for her family being in town for chance reasons and a surly drunken dwarf with "nipple clamps" passing by the farm as a first responder, none of them would have gotten back up.
Obfuscating Stupidity: MLP fans will already be familiar with Pinkie's tendency to know more than she lets on, but suffice to say that's the tip of the iceberg. Throughout the dungeon crawl she completely takes Twilight off guard as a perceptive and devious teammate, going as far as to engineer the circumstances of her own death during a bad pull (granted that she caused by accident) so she'll be in a better position to pull everyone back up after the wipe.
Only Sane Mare: Twilight in a rather specific way: she is the last to adapt to the fact that she is now essentially a MMORPG character. Especially the jargon of Pinkie Pie and Rainbow Dash has her confused.
Quirky Miniboss Squad: Blood Driver, Catnip and Sniffles and Gull act like this for the Cult, each with different level of power.
Redshirt Army: averted. Morning Star's team look like this initially, requiring the help of adventurers on all stages of preparing the assault. Once they actually go to battle however, they prove very disciplined and highly competent.
Rocks Fall, Everyone Dies: In the prologue Ponyville is wiped out by Deathwing, fortunately Celestia is there with a mass resurrection.
Shout-Out: Numerous, and almost all of them done by Pinkie Pie.
Sugar Bowl: Deconstructed. Keeping Equestria a Sugar Bowl had a price - sacrifices that had to be made and secrets that had to be kept. As the result it contributed to Start of Darkness for both Nightmare Moon and Voidhorn
Sure, Why Not?: At the conclusion of the story, the Manes get an achievement for completing the dungeon, but the author accidentally forgot to show Dash getting it too. When this was brought to the author's attention, he added an epilogue where Dash petitions a GM for it.
The Heart: - discussed. In an attempt to make Morningstar smile, Pinky Pie uses her totems for a brief Captain Planet spoof. Later, she talks about how she really is The Heart for her elemental spirits, allowing the opposite elements to work together.
There Is No Kill Like Overkill: Luna's energy blast hits Voidhorn with such power that it blasts her through several floors and nearly collapses the tower.
This Is Unforgivable: Catnip holds a dubious record of being the first person to ever provoke Fluttershy to violence.
Total Party Kill: A stray patrol pulled by Pinkie's totems at the end of a gauntlet event wipes out the party, giving Twilight her first death experience.
Twenty Bear Asses: The girls were once given a quest to find three pristine manticore tails, which end up taking them all day. And the original quest giver was still picky about how pristine one of the tails was.
Rainbow Dash: "This. Is why. I hate. PVE!!"
Worth It: WOW tanks know very well that their job is to take hits so their teammates don't have to, but it's very easy to abstract everything into your health bar and not think about that. This story pulls absolutely no punches in detailing that Applejack (and Dash when necessary) are getting skin burned off with magic, swarmed by venomous flesh-eating insects, ribs smashed and limbs dislocated several times in the space of a minute, impaled a few times, and generally getting the ever-loving horseapples beaten out of them. Continually. And yet...
Applejack: "I took a beatin' to high heaven, but Ah gotta say, it was worth every minute ta know every blow Ah took was one my friends didn't have'tah."
Dash complains a bit about it, but her reluctance to tank is zero parts "oh no, pain!" and all parts "I'd rather be hitting things."
You Fight Like a Cow: a part of warriors' taunting mechanics. Actually said word by word by Applejack (obviously, against a tauren)