The online multiplayer mode was removed in the Japanese release, same goes for Ratchet: Deadlocked.

The box art for the Japanese release is a lot more colorful and cartoony when compared to the US release. Additionally, the name was changed to "Ratchet & Clank 3" in Japan and Europe.

The Lava Gun, a weapon previously used in Ratchet & Clank 2: Going Commando, has a different final upgrade than its Going Commando counterpart. Instead of the Meteor Gun, it upgrades into the Liquid Nitrogen Gun. This was done because of fan complaints that the Meteor Gun completely changed the way the original weapon, the Lava Gun, was meant to be used.

This was the only time that a weapon imported from a previous Ratchet & Clank game had been changed.

When Ratchet and Clank meet with the Plumber in the sewers on Aquatos, he says that they are "right on schedule". In the previous game, Ratchet & Clank: Going Commando, released about a year before, the Plumber had told them that he would see them in "about a year or so".

The cover of the game was later reused in Ratchet & Clank: Going Mobile.

On the North American cover, Ratchet is holding his weapon in his left hand rather than his right.

Dr. Nefarious' attack color scheme was picked at random from a friend of Tony Garcia, the designer of the boss. Since the battle was the last thing to be programed, he was running out of ideas for colors. He picked one friend that was online at the time and asked for two colors, which they gave red and black. These random colors have stayed with the character.

Courtney Gears is a parody of female singer, Britney Spears. During the fight with her she will shout out "Oops, I did it again!"

The dune-buggy that you use on Tyhrranosis comes from an unused race feature planned for the game. One of the race tracks for the game made it to the art phase before being cut fairly early on. Space combat was also supposed to make a return, but was also ultimately cut.

If you hold down R1, R2, L1 and L2 at the title screen, a hidden demo of Sly 2: Band of Thieves will be unlocked. Successfully completing the demo will give you access to a cheat which replaces your wrench with a double-bladed laser sword.