In the stage "www.dotcom.com", there is a secret tipball, which when accessed, gives you an old web address where you had several tips and cheats of the game.

The URL has long since been defunct, but can be accessed via the Wayback Machine.

In the boss stage, "Mooshoo Pork" should the player enter into Look mode using the Triangle button and face the left area of the stage for several seconds, a sudden message in green font will come up in the upper left hand corner of the screen, citing: HOORAY FOR BUNNY GEX/HE SURE IS A FUNNY GEX/RA RA RA.

This seemingly out-of-place message is in direct reference to the bunny costume that Gex dons during the "Toon TV" stage.

In the hub world, "THE MEDIA DIMENSION", a hidden developer message can be found behind the area that hosts the entrances to three unlockable bonus stages, and can be viewed when using the Manual camera controls.

The message reads, "Jezza! rich '98, Faith, Hope, Unity."

In 2021, a widely undocumented Easter egg during the "Enter the Battle Dome" mission in "The Umpire Strikes Out" level in the Rocket Channel was uploaded to YouTube. When the player reaches the purple energy tower, you will need to climb the tower up to the square platform area with two air tanks on it. Just to the right of those air tanks, an invisible path marked by vague star textures and small red lights will appear in view once reached, leading to a hidden area with a floating metallic cube featuring a photo of programmer Evan Wells behind a blue background. Like the production baby cameo found in the same level, the object will slowly spin around showing the photo on each side, can be jumped on, and can be destroyed with Gex's attacks.

In 2020, a widely undocumented Easter egg near the start of "The Umpire Strikes Out" level in the Rocket Channel was uploaded to YouTube. From the level's checkpoint, there is a platforming section consisting of floating metallic walkways. If the player karate kicks from the second walkway into the abyss, you should land on a mostly invisible platform, only marked with vague star textures and small red lights. Going south of the platform will lead the player back to the start of the level. If the player goes north, mindful that you jump over a hole in the platform on the way there, a small area can be found that contains an oxygen tank, some crates, two Green Fly TVs, and a floating metallic cube with an image of a newborn's face on two sides. The cube will spin in place slowly unless the player destroys it with Gex's attacks. The cube even has some collision that allows the player to jump on top of it. It's unknown who this infant is, but it is presumably a production baby raised by one of the game's developers.

At the end of the game, Nikki from the Pandemonium series can be briefly seen in Gex's hotel bed.

In the American release of the game, Gex is voiced by comedian Dana Gould. However in the European release of the game, Gould's voice was replaced by that of English actor Leslie Phillips, who provided a very different, more cultured and refined variation of the character.

In the bonus level, "Chips and Dips", developer photos with humorous text can be found across the stage. A photo of producer Jeffrey Zwelling was found during gameplay by accident, and to date, the criteria to activate the picture is uncertain.

In the PlayStation version, one of Gex's quips is "I guess Bowser's on vacation?", referencing the main antagonist of the Mario franchise. Ironically, this line doesn't appear in the Nintendo 64 version of the game due to many of Gex's lines having to be cut due to storage limitations on N64 cartridges.