- Goggles at one point pulls out a disintegrater gun from out of nowhere and tries to use it to destroy a Mary Sue Stunfisk. The gun disintegrates.
- Einroth is a shout out to both Final Fantasy VII's Sephiroth and ThoseLackingSpines's Jeffiroth.
- There are several shout outs to My Little Pony: Friendship Is Magic... err, My Little Blitzle in the earlier arcs.
- Homestuck shout outs: They keep happening.
- PEFE HQ in the AU is one giant shout out to Portal and its sequel.
- The entire Goldenrod Nidoran Colony is a shout out to Watership Down.
- The Angela of PMD-B is based on Fallout.
- Many videogame products or franchises are referred to by alternate names, such as "Grasswhistle of the Eons". There's a full list here.
- The entire Return To Dreamland arc is a Shout-Out to...yeah.
- A sideplot in the AU Haruba Desert shows that the place has become Dry Dry Desert.
- Dune's team includes Pokémon named Laharl, Flonne, Etna, and Champloo. He also has Pokémon named Big Dom and Garuda.
- Deziree, on top of being a visual Expy of Agatha Heterodyne, has Pokemon named Wuffles, Doofenshmirtz, Norm, DOCTOR MOBIUS!, and Cid.
- Aline going Hoenn confirmed.
Shout Out / We Are All Pokémon Trainers
Here are just some of the many references We Are All Pokèmon Trainers has made to other works.