In a preview build of the game, it was possible to play as Jak from Jak II. Although this Secret is not present in the final version, it's still possible to trigger it by editing the game's memory, in the same place Secrets are kept track of.

In an earlier version of the game's plot, it was Jak's Light Eco transformation that would cause the Day Star to appear in the sky. In it, the Precursors would come to rebuild the planet and declare that only the fittest species would be allowed to remain. In this iteration, Spargus and Haven were warring factions.

After defeating the game's final boss, by using debug controls and using the free camera mode during the game's cutscene, you can actually see Jak & Ashelin Praxis kissing onscreen, rather than cutting to Daxter. Often these scenes would not be fully animated, but the character expressions change where they would usually not be seen.

There is a hidden picture of the Naughty Dog developers' team and is accessible using a flying glitch.

In the Freedom HQ, you can find a series of screens that have some Precursor text scrolling on them. When translated, the text becomes a farewell message to Naughty Dog's pet/mascot, Morgan, who died at age 13.

Naughty Dog's name was inspired by their first company mascot Morgan, a Labrador/Rhodesian Ridgeback mix born in 1989 who was the pet dog of co-founder Jason Rubin starting with the development of Rings of Power. During the development of Way of the Warrior, Morgan lived with both Rubin and co-founder Andy Gavin in poor living conditions and she was often fed some of their meals from the fast food chain McDonald's. While she first appeared in a game as a Special Thanks credit in Rings of Power, Morgan technically became part of the company when she was given her own photo ID card after Naughty Dog moved onto the Universal Interactive Studios premises for the development of Crash Bandicoot. She was credited as a member of Naughty Dog on their four Crash Bandicoot games and Jak and Daxter: The Precursor Legacy. She died in 2002 at the age of 13 during the development of Jak II, and several tributes to her were put into Jak II and Jak 3.

Jak II's manual and end credits feature a standard In Memoriam dedication for Morgan, but there are two more hidden tributes in the game. There is a green neon sign spelling Morgan's name written in the Precurian language inside the Hip Hog Saloon located to the left from the door. Additionally, in the Power Station in New Haven City, a set of random scrolling Precurian messages can be found on the large computer monitor. Translating these to English will reveal the following:

• "Morgan I miss you"
• "Morgan"
• "Thirteen years hard time"
• "There will never be another"
• "Good dog"
• "I will always love you"

Another message can be found on computer screens you can view at eye-level, which reads "Morgan is still missed even after a year has passed". These computer screen messages are re-used on the monitors in both the Power Station and the Freedom League buildings in Jak 3. Since Morgan's death, Naughty Dog have credited more pets as members of their team and/or company mascots, with the first successor being a Labrador puppy named Osiris who first appeared in the credits of the first Jak and Daxter game alongside Morgan.