In the boss fight with Tiny in Crash Bandicoot: Warped, if you stand in the top left corner of the arena as the lions are coming out, the audience will start throwing cheese at you. A reference to a glitch found in the original version of the game.

During the intro cutscene of Crash Bandicoot 2: Cortex Strikes Back, Naughty Dog's paw icon can be seen on a passing asteroid.

During the intro cutscene of "Crash Bandicoot 2: Cortex Strikes Back", Coco Bandicoot is watching a cutscene of Nate and Elena from Uncharted 4: A Thief's End on her laptop, playing the original Crash Bandicoot on the original PlayStation.

During one of Coco's idle animations, you can see the Crash Bandicoot sub-reddit on her laptop.

Inside Crash's home during the opening and ending scene of "Crash Bandicoot 3: Warped", you can see picture frames of "Nathan Drake" from the Uncharted 4: A Thief's End and "Tawna Bandicoot" from the first game.

While waiting for one of Coco's phone idle animations, her phone will start to spark and then she'll toss it away right before it explodes. You can also break any boxes, even kill yourself if TNT or Nitro are caught in her phone's explosion.

Coco's laptop and phone displays stickers featuring the "Naughty Dog" and "Vicarious Visions" logos.

In all the racing levels of Crash Bandicoot 3: Warped, if you look closely at the registration plate of the opponents' car, it reads "96-17".

These 2 numbers are references to the years of the release of the original Crash Bandicoot in "1996", and the remake trilogy in "2017".

In the Egyptian-themed levels, there are hieroglyphs of black dogs on the wall that are speculated to represent Morgan, the first pet mascot and original namesake of Naughty Dog. The N. Sane Trilogy remake of the game kept this reference intact.

If the player completes the whole trilogy in 100%, they'll be able to see "Fake Crash" in some of the levels. This includes:

"Crash Bandicoot"
N. Sanity Beach: At the left side of the stone stairs.
Heavy Machinery: In one of the pipes near a platform that takes Crash down to a different path.

"Crash Bandicoot 2: Cortex Strikes Back"
The Pits: At the left side of the path, near the first big mushroom, right after the split path ends.
Crash Crush: On the left side of the path while Crash is getting chased by a boulder.
Hang Eight: At the end of the Blue Gem route, on an un-reachable platform with two Venus Fly Trap enemies.
Ruination: At the right side of the first platforms moving in circle.
Cold Hard Crash: In the first ice mirror in the death route.
Rock It: At the right side of space, in the first glass room.
Totally Fly: Between a tree and a tiki statue on the left.

"Crash Bandicoot 3: Warped"
Toad Village: On the lawn, enclosed in a fence, of the 3rd house on the right. There is a pond in front of the house where Crash can walk on.
Makin' Waves: On a small island with grass, and a palm tree, at the end of the level, on the right.
Hog Ride: Seen dancing on the left side of the road. He is in between the gas station and the Cortex sign, near the two ramps right next to each other.
Area 51?: Left side of the road near a tall cactus, on a left turn.
Future Tense: Near the end of the death route, on a building to the right.

At one point, the official Spotify, Apple Music, and YouTube releases of the song "Bone Yard" from Crash Bandicoot N. Sane Trilogy opened with a GEICO insurance commercial as part of the song. This seemed to have not been part of its initial upload in 2017, and has since been fixed.