Here is a list of easter eggs I have found in Pegasus Prime. The majority of these will be accessed by holding/pressing the E key in various places. These will be listed in chronological order based on game progression. Oh and I don't think I have to mention this, but there will be SPOILERS in this guide.

If you want to find these on your own, you shouldn't be here.

#1: Interface overview
Location: Interface overview
Click on the E on the keyboard (or the Select button if you are using Steam controller)

#2: Radio Wakeup w/ Buzzer
Holding E during the intro movie into the waking up cinematic will initiate an easter egg of an alarm clock buzzing as well as a radio voice talking (from the classic JMAN1).
Holding E must be initiated during the intro movie, not on the title menu. The movie cannot be skipped.

#3: Month-o-Matic
Holding E right after the initial video call ends (when you are first waking up) will initiate the Month-o-matic easter egg.
Be sure to hold E as soon as the video call ends. You can skip this video call if you don't want to watch it.

#4: Arthur AI Biochip
Holding E and pressing the lowest button on your food replicator (the one that usually spawns the orange beverage) will spawn a cornbread instead of the usual glass. Clicking on this cornbread will initiate a movie, and aquisition of the Arthur AI Biochip.

#5: Classic Elevator Voice
Holding E as you press either the 2 or 3 floor buttons in the elevator will play the classic voice from JMAN1.

#6: Alternative Jimenez
Holding E as you click on the Jimenez head in the TSA entryway will play an alternative dialogue.

#7: Alternative Castillo
Holding E as you click on the Castillo head in the TSA entryway will play an alternative dialogue.

#8: Alternative Matsumoto (STEAM VERSION ONLY)
Holding E as you click on the Matsumoto head in the TSA entryway will play an alternative dialogue.

#9: Alternative Sinclair
Holding E as you click on the Sinclair head in the TSA entryway will play an alternative dialogue.

#10: Alternative Walchek (Laughing)
Holding E as you click on the word "Walchek" on Sinclair's answering machine in his office will play an alternative dialogue.
You will need to transfer his messages to his office from the room you spawn in when you first get to WSC.
This easter egg is a random occurrence and you can sometimes get #11 instead.

#11: Alternative Walchek (Exploding Implant)
Holding E as you click on the word "Walchek" on Sinclair's answering machine in his office will play an alternative dialogue.
You will need to transfer his messages to his office from the room you spawn in when you first get to WSC.
This easter egg is a random occurrence and you can sometimes get #10 instead.

#12: Hidden 4th Sinclair Entry
Holding E as you click slightly below the 3rd entry on Sinclair's computer (below the assault rifle) will play a lengthy 4th entry, which is also in JMAN1.
Best way to approach this is to come up from the bottom and as soon as you can click (with a pointer finger), do so. It's right below the words "Time Bending".

#13: Spinning Globe
Holding E while clicking anywhere on the globe during the missle silo globe puzzle will initiate the spinning globe easter egg.

#14: Alternative Robot Voice
Holding E as you encounter the robot right before the shield generator will cause the robot to have a more human-like voice.
To best get this one, hold E as you are turning in the direction of the Shield Generator door.
This easter egg is a random occurrence and you can sometimes get #15 instead.

#15: Faster Walking Robot
Holding E as you encounter the robot right before the shield generator will cause the robot to walk towards you faster.
To best get this one, hold E as you are turning in the direction of the Shield Generator door.
This easter egg is a random occurrence and you can sometimes get #14 instead.

#16: Alternative Ambient Maze Music
Holding E as you first enter the maze from the airlock will constantly play the ambient maze music instead of the classic music from JMAN1.
The classic more upbeat music was initially planned as the easter egg music but was changed. The ambient maze music was supposed to be the default.

#17: Faster Flight FMV, Classic Music
Holding E before the Mars flight sequence from the Airlock will cause the flight FMV to be automatic, as well as a lot faster and having the classic music from JMAN1.
It is best to start holding E as soon as the man says "Prepare for drop launch, all clear for take off" and don't let go until the easter egg activates.

#18: Different Flying Music (PSX Audio) (STEAM VERSION ONLY)
Holding E before the Mars flight sequence from the Airlock will cause the music to change to an alternative song taken from the unreleased PSX version of the game.
It is best to start holding E before Gage swings around in the shuttle seat and before you hear "Cockpit module boarding sequence complete". Release after this line, do not hold too long or you might trigger #17.

#19: Mooed Down Death Screen (STEAM VERSION ONLY)
This easter egg is ONLY available after resolving all temporal rips. Two ways to trigger this easter egg:
From the TSA transporter: Holding E while clicking on the "Other..." option instead of clicking Caldoria Heights
From the Caldoria transporter: Holding E while clicking on the "Other..." option instead of clicking TSA.

#20: Classic Card Bomb Voice
Holding E as you plug in the card bomb on the rooftop will play the classic "Card bomb activated" voice from JMAN1.

#21: Alternative rooftop bomb music (STEAM VERSION ONLY)
Holding E as you start the bomb minigame on the rooftop will change the music.

#22: Extended Agent 8 & 5 Conversation
Holding E when you click Continue on the last Result screen will cause an alternative ending movie, with an extended conversation between Agent 8 and 5 in 5's living room. Best to hold E until the video starts playing.