Each character in the series is made to be a parallel of a character from the Half-Life/Portal universe.
Twilight is Chell.
Dr. Whooves is Gordon Freeman.
Trixie is Mel.
Fluttershy is the Companion Cube.
Pinkie Pie and Rarity are personality cores.
Rainbow Dash and Applejack are Atlas and P-Body
DISCoRD, CELesTIA, and LUNA are variations of GLaDOS.
Apple Bloom, Sweetie Belle, and Scootaloo are sentry turrets.
Cranky Doodle is Cave Johnson.
The Changelings represent the Combine.
Each episode is inspired by parts of the Half-Life/Portal games.
"Unforeseen Consequences" is based on a short segment from Half-Life and slightly on Portal: Prelude.
"Wake-Up Call" is based on the first few levels of Portal.
"The ARK" is based on the abandoned test chambers from Portal 2.
"Malicious Intent" is based on various levels and cut content from Portal 2.
"Heart of Darkness" is based on the Combine invasion before Half-Life 2.
"Tunnel Vision" is based on the old Aperture levels of Portal 2 and F-STOP.
Derpy is hidden somewhere in every episode.
EP1: In a picture on Dr. Whooves' desk.
EP2: In a cryo-chamber.
EP3: In a jar on the shelf.
EP4: In a broken picture on a desk.
EP5: On a book in the library.