In the Insomniac Museum, you can find two hidden developer areas where you can walk around two minigames, but they cannot be played there. Elsewhere in the museum, you can find two specific computer monitors with still images of passwords that can be used to play these minigames (including the spaces): " MEGHAN " and "YING TZU". The identity of YING TZU is believed to be Ying Tzu Lin, a college classmate of gameplay programmer Kenneth Strickland, while it's unknown who MEGHAN is.

These passwords can be entered by pressing Square when in front of the VG-9000 in the Starship Phoenix. Entering YING TZU will unlock "Bombs Away!", a Bomberman clone that can be played with up to four players using a multitap. Entering MEGHAN will instead unlock "Pirate vs. Ninja", a two-player fighting game between a Ninja bot and Captain Blackstar, a space pirate character who was originally planned to be the boss of the first Qwark vid-comic.

An unused unique type of crate is hidden in two locations in the final version of the game, but are invisible and can only be activated with the use of a level editor. Known as the "Upgrader Crate", the concept would have been to instantly upgrade Ratchet's lowest level weapon currently owned by one level upon breaking it.

According to Insomniac Games Developer Mike Stout, the concept was scrapped on account of detracting from the fun of using the weapons to gather XP and grind the levels/evolution into said weapon's evolved form.

The crates can be made to appear in Holostar Studios and on board the Phoenix during the rescue mission at the games climax.

Unused text in the game's files indicates that at one point in development, the developers had considered including a "Statistics" menu which would keep track of an assortment of miscellaneous in-game information, as follows:

Bolts earned
Number of enemies killed
Damage taken
Bolts spent on ammo
Shots fired
Damage dealt
Bolts spent on weapons
Nanomites (XP) earned
Time spent in Vid-Comics
Fastest play-through time
Number of objects broken
Time spent strafing
Time spent in 1st person mode
Time spent falling
Number of jumps performed
Number of deaths

This feature was likely scrapped early in development as no menu textures exist for this screen nor any option related to it in the Pause menu.

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.