The Beard: Pokey's introduced as such, when he acts as Rainbow Dash's boyfriend/date for the Starlight Dance when Dash tries to stop the rumors of her sexuality. It nearly backfires when Pokey decides to blackmail some nookie out of the deal.
The Cameo: Almost all the background ponies in the comic are actually fan-submitted O Cs.
Creator Cameo: SorcerusHorserus's ponysona appears in chapter six drawing a sketch of Derpy and Surprise.
Expy: Surprise is pretty much a pegasus version of Pinkie Pie. Also doubles as a Mythology Gag.
Fair Weather Friend/Vitriolic Best Buds: Gilda plays pranks on Dash, ditches Dash when invited to go with the Speedster's team, blows off Dash's justified concerns that Billy's screwing with her, and tells Dash to deal with her own problem with Pierce instead of helping her create a distraction. But Gilda's also seen trying to comfort Dash when she's worried that she won't be able to get a scholarship, holds her back to keep her from attacking the coach, and tells Pierce to buzz off when he tries to force the issue with Dash.
Mythology Gag: Two of the Junior Speedsters, Surprise and Firefly, are basically exported straight from G1 My Little Pony series, with Surprise being the proto-Pinkie personality that Lauren Faust had intended to use.
Ship Tease: As of recently, Fluttershy and Brolly have been shown together quite a few times. One can only imagine...
The Unsmile: At the dance, Fluttershy tries to sit quietly and smile. When she smiles with her teeth exposed, her braces make her look weird. When she tries smiling without the braces, she looks creepy.
What the Hell, Hero?: Firefly calls Dash out for her attitude toward Derpy. Dash isn't really affected because she doesn't see herself as unfairly singling Derpy out as she doesn't know what's happening with Derpy, and her own dreams of getting a college scholarship were getting crushed because she herself was unfairly singled out.