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, the former gives what is described as "the longest series of curses in pony history".
Heel-Face Turn: Ratchet the manticore, though she was never evil in the first place.
Informed Ability: Quill is an author and Filter is a musician. We have yet to see either of them actually perform these talents. Justified, as the talents are based on the talents of the respective authors rather than having any specific impact on the story.
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.
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.
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.
StealthPunny Name: Pop Filter; a pop filter is a microphone attachment, so this seems to be a reference to Filter's musical 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.