1. Coco's idle animation in Crash Bandicoot N. Sane Trilogy has her opening her laptop and going onto the Crash Bandicoot subreddit board

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...and in the opening cutscene, it looks like she was watching the Crash Bandicoot scene from Uncharted 4! 
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2. The announcer in Sonic & All Stars Racing Transformed will beg you to stop if you start turning down the volume of his voice in the sound settings





3. In Ratchet & Clank the player is told that their employee discount at Gadgetron will only kick in after 2 years... if you still have your save file by the time you bought Ratch & Clank 3, this message appears:

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4. The bottle of wine next to Campbell in Dishonored will not appear in his portrait if you decide to steal it earlier in the game

Dishonored
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5. If you lose your humanity and go hollow in Dark Souls 3, your character will no longer cast a shadow

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6. While escaping from the new installation in Halo 3, you drive around an island that's nearly the same shape as the one from The Silent Cartographer mission from Halo: Combat Evolved

halo silent cartographer halo 3 easter egg

 


7. The low-poly cockroaches from Half-Life 1 have their own A.I. system to ensure they act properly roach-y

 


8. Before fighting Dark Link in Ocarina of Time, you can see Link's reflection disappear.

 


9. In the music track "Cyberdemon" from the 2016 DOOM remake, you can see the number of the beast and a pentagram when running the sound through a spectrogram

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10. Back to Halo 3, you can see that Master Chief fires personalized "CHIEF EG-X" ammo.

ammo ammo halo ammo
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11. In your asylum cell from the first Dark Souls, there are actual polygonal dookies in the chamber pot that cannot be seen without hacking the in-game camera

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12. In the Witcher 3, you can actually receive a thank you note from Millie if you come back to Oreton after successfully returning her to her family.

Millie