Big Damn Heroes: A minor example. When Quill is being harassed by Jack Ass, a fake royal guard trying to get some bits, Filter sees the commotion and heads over. It's unknown what would've happened if he didn't step in, but as it is, he managed to bribe Jack Ass into going away and save Quill from further trouble.
Blind Without 'Em: Filter — literally, as his glasses are enchanted to counter the damage caused to his eyes by the Days of Discord.
Break the Cutie: Happens to both Quill and Filter in their backstories, but doubly so for Filter.
Chaste Hero: Filter doesn't realize Pinkie's crush on him, despite it being about as obvious as Spike's crush on Rarity.
Cluster F-Bomb: When Quill and Filter realize that the house they've just bought has a caved-in roof, he gives what is described as "the longest series of curses in pony history".
Defeat Means Friendship: After knocking out a manticore in the Everfree Forest, Quill and Filter befriend her and take her home rather than killing her or leaving her in the forest.
Demonic Possession: Sort of. King Sombra somewhat possesses Filter, but at the moment, Filter hasn't changed much. However, if Sombra isn't removed soon, he'll apparently corrupt Filter.
Deus ex Machina: Filter at the end of chapter 7. He just shows up, solves the Pinkie Pie clone problem with a simple question, and walks away with the real Pinkie to let Twilight zap the others. Though to be fair, this happened right before Twilight could begin the "test" from the actual episode, so the result would have been the same either way.
Disappeared Dad: Filter's father vanished when he was a child. Then one day, he came back just to kill Filter's mother and then himself.
Failed a Spot Check / Unusually Uninteresting Sight: When Quill and Ratchet are rounding up the Pinkie Pie clones, nopony points out Ratchet, despite her being a manticore in a town of ponies. Justified, as it was implied they were paying more attention to the Pinkie Pie clones, and Ratchet was hiding for the most part after things calmed down.
Felony Misdemeanor: Filter overreacts a bit when recounting to Quill how Rarity forced him to wear a suit.
Foreshadowing: During an argument between Quill and Filter, the latter states how earth ponies are physically the strongest and most durable of the three main pony types and unicorns are the weakest. Later on, Celestia and Luna explain to Filter that, being a unicorn, surviving the jump from the top of the Crystal Palace would have been impossible, while earth ponies or pegasi may have survived.
Got Me Doing It: Over the course of a conversation with Zecora, Filter ends up adopting her Rhymes on a Dime method of talking until Twilight points it out.
Informed Ability: Quill is an author and Filter is a rapper. We have yet to see either of them actually write or rap.
Insane Troll Logic: When Filter accuses Quill of never thinking, Quill comments that despite that he's still alive, opposed to beings Discord or Nightmare Moon, who did think and are now as good as dead, and that thinking is therefore the cause of death. Filter is left dumbfounded.
Monochromatic Eyes: Somewhat with Quill, whose eyes are almost completely white and/or gray.
Mood Whiplash: The first chapter starts with Quill and Filter joking around and arguing...then Quill makes a comment about a past event, and Filter recoils at the memory, leading to a slightly sad yet heartwarming moment. Then they're right back to arguing.
Chapter 1 is pretty much all comedy. Chapters 2 and 3 feature Quill and Filter's rather sad and dark backstories. Plus, in chapters 2 and 3, the scenes alternate between the past and the present, so you go from hearing about Filter's mother being murdered to Quill complaining about grammar.
Near the end of chapter 6, Quill is upset because he thinks Filter's dead...only to cheer right back up when Filter comes back, seemingly fine. Then it switches back to being dark when Filter discovers his hazel eyes have gone red, a voice speaks to him from nowhere, and he bursts into the castle to scream at the princesses.
Ship Tease: Rarity squealing over how good Filter looks in a suit during his (somewhat unwilling) visit to Carousel Boutique. This continues later at Quill and Filter's welcome party.
There's also a lot between Filter and Pinkie. Quill even points it out frequently. Then they finally get together.
Shout Out: The beginning of chapter 4 appears to be a reference to The Hangover. Quill wakes up with no memory of what happened the night before, wonders where Filter is, and proceeds to find him on the roof of Sugarcube Corner.
Dual Image might as well be renamed "The Doctor WhoShout Out Chapter". Not only do Quill and Filter quote the Doctor various times, the scene where Filter, powered up by King Sombra, completely overpowers Trixie and forces her to surrender before forgiving her is taken straight from Last of the Time Lords.
Sleazy Politician: Mayor Mare is a downplayed example. She hires Quill as a mercenary to stop a manticore in the Everfree Forest, then demands her money back when it turns out he didn't actually kill the manticore.
Stealth Pun: The title of chapter 8: "Love is in the Ground". Filter and Pinkie, two ground-bound ponies (unicorn and earth pony respectively), get together in this chapter.
StealthPunny Name: Pop Filter; a pop filter is a microphone attachment, so this seems to be a reference to Filter's rapping ability. However, another name for a pop filter is a pop shield, and a shield is part of Filter's cutie mark due to part of his special talent being protecting others.
You Are Better Than You Think You Are: Filter, sick of Quill's self-pity, yells at him and basically tells him this. Not only does it snap Quill out of his depression, it somewhat angers him, causing him to stand up and yell right in Filter's face. Knowing Filter, you'd expect him to cower...but he doesn't.