I've had this kicking around as I played sooo.. here we go! I don't 100% remember all the spots they were at though.
Non-Pokemon References
Batman - There is a female Team Flare Grunt who seems to act a bit like Harley Quinn.
DBZ - The over 9000 joke.
Stayin alive - grunt sings it
Yu-Gi-Oh! Abridged Series - Punk says his hair gives him super power.
101 Dalmations - "you know, when i leave home every morning i kiss every one of my 101 Furfrou good bye."
Daft Punk - Essentia's outfit resembles the Daft Punk suits.
JoJo's Bizarre Adventure - Pangoro is clearly inspired by Banchous. Specifically Jotaro Kujo. (Many of the artists that work for Game Freak are also huge fans of JoJo's Bizarre Adventure. Their tweets upon the 2012 anime's reveal were filled with fanboyism. )
Mega Man Star Force: Shiny Aegislash and Shiny Tyrantrum have matching colours to Rogue and Megaman. While not shiny, they both suit the Zerker X Saurian theme with matching colours. Designed by Hitoshi Ariga of Mega Man manga fame.
Canon Pokemon Series References
Pokemon ReBurst - A scientist mentions the device used in ReBurst.
Pokemon Origins - A trainer says their Pokemon's nickname is Sepultura.
Non-Pokemon References
Batman - There is a female Team Flare Grunt who seems to act a bit like Harley Quinn.
DBZ - The over 9000 joke.
Stayin alive - grunt sings it
Yu-Gi-Oh! Abridged Series - Punk says his hair gives him super power.
101 Dalmations - "you know, when i leave home every morning i kiss every one of my 101 Furfrou good bye."
Daft Punk - Essentia's outfit resembles the Daft Punk suits.
JoJo's Bizarre Adventure - Pangoro is clearly inspired by Banchous. Specifically Jotaro Kujo. (Many of the artists that work for Game Freak are also huge fans of JoJo's Bizarre Adventure. Their tweets upon the 2012 anime's reveal were filled with fanboyism. )
Mega Man Star Force: Shiny Aegislash and Shiny Tyrantrum have matching colours to Rogue and Megaman. While not shiny, they both suit the Zerker X Saurian theme with matching colours. Designed by Hitoshi Ariga of Mega Man manga fame.
Canon Pokemon Series References
Pokemon ReBurst - A scientist mentions the device used in ReBurst.
Pokemon Origins - A trainer says their Pokemon's nickname is Sepultura.