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.