Archive Panic: Something shared with its parent series. With ten "episodes" made of multiple parts (The tenth episode itself has over ten parts) and the submission/discussion-in-comments nature of the story, there's quite a lot of material to read.
Fanfic Fuel: A lot of the universes depicted in the What If Machine. The universe created by Red Gala's existence also qualifies.
Harsher in Hindsight: After one session with the What If Machine where Twilight battled Morning Star in a world literally shaped by the beliefs of mortals based loosely on Shin Megami Tensei, the girls gave commentary with Rarity mentioning that she's "all for faith and love giving somepony strength, but I'd rather not become a mean old nag simply because everypony else thinks it's true." Nyarlathotrot and Discord would later concoct a reality-warping plan that would result in exactly that and then some in the Rumors Arc of the Parent Series.