In the Japanese version, when Jak and Daxter falls into the Dark Eco, it utilizes 2 audio files, but in the other versions, it utilizes 3, ultimately making the sound effect different in Japan exclusively.
In the HD collection the trophy named "shiny happy steeples" is a reference to the R.E.M. song "shiny happy people".
Naughty Dog made a web-based browser game, The Lost Levels, which was said to be based on the game's early production in the 1990's.
It was later revealed by Naughty Dog that Jak's uncle, the Explorer, was created before the plot of Jak II was created, and he was intentionally not mentioned again after the events of the first game to avoid creating continuity errors.
During the final battle Spoiler:with Gol and Maia, they will start bantering with the player. One of the things that Gol will say is "We're not gonna take it!". This would be a reference to the Twisted Sister song of the same name, as Gol is voiced by Twisted Sister frontman, Dee Snider.
The Venus Fly Trap enemy from the Crash Bandicoot series can be seen at the start of the game inside Samos' hut as a decoration.