Using the dynamo on the game pyramid in clank's apartment will start the "Sheep Blasters" mini game without having to beat the game first. This mini game is unlocked normally by simply beating the game for the first time.

The Binary on the signs on Planet Notak spell Dan and are homage to Dan Johnson.

On Planet Damosel, after completing the grind sequence and receiving the Hypnomatic part, Clank will do the same dance as Daxter from Jak and Daxter.

In the Insomniac Museum, on the opposite side of the Grav-Ramp tower, a floating face of Dan Johnson (the same as the Snow Dan) can be found.

On planet Boldan, if the time is between 3am and 4am, a secret teleporter hidden on top of a fountain will become accessible and allow access to the Insomniac museum.

The final level was going to have a Clank traversal segment to help Ratchet go further into the level, and would reintroduce the lifter bot for a few more puzzles. However due to memory restraints and time, the segment was scraped and the lifter bot was reduced to an only one time use in the first Clank segment.

The name of Megacorp's CEO, Abercrombie Fizzwidget, is a parody of the popular clothes brand Abercrombie and Fitch.

On the TV in Clank's apartment, there is a picture of Jak and Daxter from Jak 2.

There is a snowman in both this game and Up Your Arsenal named Snow Dan. This is an in joke for the developers which references a former Insomniac Games employee, Dan Johnson. Also, the Insomniac Museum planet, Dantopia, was also named after him.

The "Game Pyramid" that you find in Clank's room once started out as a PlayStation 2. However, the PlayStation TRC states that you can not have a PS2 in your game that you can destroy. It was than replaced as an X-box, but was taken out as they were not allowed to have a competitor's machine in the game.

At the title screen, Ratchet is seen playing levels from the game. If you sit around on this screen, he will start playing levels from Ratchet & Clank, Jak and Daxter: the Precursor Legacy, Jak II, and Sly Cooper and the Thievious Raccoonus.