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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.
Contributed by ProtoSnake
There is a hidden picture of the Naughty Dog developers' team and is accessible using a flying glitch.
Contributed by nedved
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.
Contributed by gamemaster1991