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.

In the North American release, the cover art is reversible, with the back side featuring a map of Haven City. The front of the game's manual points this map out as a tip to players, but the Greatest Hits re-release of the game did not include this map, with the manual not being updated to reflect this change.

Throughout the Jak and Daxter series, a fictional, translatable language appears in a variety of environments known as Precursor. Official guides often included legends that enabled players to translate signs in the open world Haven City and other instances of Precursor, often discovering easter eggs in the process.

For an unknown reason, exclusively to the 2012 PlayStation 3 port of Jak II released in the Jak and Daxter Collection, a particular texture on a barrel of Dark Eco appearing in the Drill Platform stage was altered; originally, in the PlayStation 2 version of the game, the barrel read "Barrel of Eco" in Precursor. In the PlayStation 3 version, the same Precursor text now instead reads "Barrel of Shit", and was possibly changed to mess with anyone diligent enough to translate Precursor in the middle of gameplay.

There is a Precursor orb hidden out of bounds underneath the Underport stage that can be collected using a documented hovering glitch with the JET-Board found in both this game and Jak 3, or through the game's debug mode.

There is a glitch whenever Jak walks in front of a mirror that causes a slightly different model of Jak with dark grey horns to appear alongside the "reflected" second model of the room, initially suggesting that Jak was used as a test model for shaping Dark Jak's horns. However, a 2003 promotional contest advertisement hosted by Cartoon Network's programming block Toonami features a higher resolution model of Jak with white horns instead, suggesting that the model sent to Cartoon Network still had the horns on them and they just altered the model for the advertisement, or that Jak was originally supposed to have visible horns like Dark Jak.

Although not referenced in game, Pecker is a Monkaw (half monkey and half macaw).

During development, early ideas for new eco powers revolved around time manipulation. Although unused in the final version of the game, these eco powers are present in a preview build - Jak would've been able to manipulate time by accelerating it (increasing his movement and firing speed), decelerating it (slowing enemies down), or stopping it altogether.

One mission went completely unused in the final build of the game, having Jak and Torn protect the city wall from a Metal Head invasion. The fight would end with Torn revealing his tatoos symbolize the guards' loyalty to the city.
The mission is present in a preview build of the game, complete with character dialogue and ending cutscene.

Design documents show that the relation between Jak and Mar was to be explored in more depth before the end of the game. In early plot revisions, Jak and Sig would discover Mar was a time traveller who vanished after founding the city.
Mar's time travelling device would've been found in the Underport.

The earliest iteration of Dark Jak would've made him faster, completely invincible and able to use items that would otherwise hurt Jak.
This would come with the added drawback of always ending the transformation with one hit point left.

Each civilian vehicle has its own name: One-seater vehicles are Zoomers, two-seaters are Flyers and three-seaters are Cruisers.

"Construction Site" is a relatively unimportant level in the game, with only a cutscene being played there and little else for the player to do. It is very likely, however, that this level was at one point meant to have a bigger role in the game. The level has a lot of collision at places that are not normally reachable, and there are text entries for unused mission names, including "Climb Construction Site" and "Find Baron at Construction Site"

There is a picture of the Naughty Dog developers hidden out of bounds inside a building in Haven City.

Near the stadium is a billboard of Ratchet and Clank from their appearances in Ratchet & Clank: Going Commando.

Sandover Village can be accessed and explored though a glitch in the first cutscene. However, since the area was only meant to be used in said cutscene, the village does not have any characters and the levels Forbidden Jungle, Geyser Rock, Misty Island, Sentinel Beach, and Fire Canyon are inaccessible as there is nothing to call up for these areas.