Yang's pun in season 2 chapter 1 "I always start my semester off with a yang" reflects her voice actor, Barbara Dunkleman's, penchant for puns.
In Volume 2, Chapter 4, Sun and Neptune are found at an Asian food stall named 'A simple wok'. This is a reference to another Rooster Teeth program, A simple walk into Mordor.
During the dance, at least 3 different hair models can be seen from the 3D modeler Kozaburo. These were made for the 3D program Poser years ago, but have been popular ever since.
In Volume 2, Chapter 2, Mercury and Emerald joke about another character being "some kind of cat. What, like a Puma?". This is a quote from another Rooster Teeth series, Red vs Blue, where the "Warthog" vehicle is said to look more like a Puma in an early episode.