Anti-Climax Boss: The final boss, which can be fought using a hovership. The problem is all of the boss's attacks are telegraphed and are slow-moving projectiles, so they're easily avoided with the same strafing and dodging techniques you've used in previous hovership missions.
Best Boss Ever: The final boss fight against Dr. Nefarious is an awesome, intense fight. After the extreme difficulty of Drek and the pushover of the Giant Protopet, Nefarious hits the sweet spot between the two, possessing attacks that force you to stay on your toes, and won't punish you overly if you mess up. It's nice in concept as well — Nefarious might be a bumbling fool while in cutscenes, but when he's forced to fight, he's very capable of holding his own.
Best Level Ever: The assassination mission on Planet Aridia. With great music and an expansive enviroment, there are many ways to approach this level, whether it be using sniper rifle stealth or just outright going in with a destructive vehicle.
Ear Worm: Just try to get that Courtney Gears song out of your head. It doesn't help that it gets both a Boss Remix and a Groovitron remix in Tools Of Destruction.
Even Better Sequel: It takes Going Commando, trims the fat, and refines the heck out of everything else. Add the surprisingly good multiplayer, and the result is a game that's usually regarded as the best of the series. The only general complaints are how short and easy it is compared to the previous games.
Game Breaker: In contrast to Going Commando's first-game weapons, all of the Old Save Bonus weapons in this game are extremely powerful.
The Mini-Turret glove launches an automated turret to attack, the turrets are powerful, target enemies on their own, are invincible, and you can have several out at once. The only downside is the limited ammo, but it's so good that you'll mostly only need to use one to take out a group of enemies anyway.
The Lava Gun can still destroy enemies quickly, and retains its constant stream properties when it upgrades this time, meaning that it remains an excellent crowd controller.
The Bouncer retains this status from the previous game, despite having less ammo this time around. It can clear out a group of enemies with the initial bomb, and if another group comes in, they'll be taken out by the bomblets left behind. It also works extremely well on powerful enemies.
The Plasma Coil isn't too bad initially, but once it becomes the Plasma Storm, it fires an orb that zaps everything in its path. Little enemies have no chance of reaching you, and one or two more will take care of the rest with ease.
The Shield Charger outclasses the Holoshield in every aspect, as it surrounds you directly as opposed to putting up a stationary barrier. It can soak up a lot of damage, so stray fire isn't as threatening. Once it becomes the Tesla Barrier, it'll also zap any nearby enemies, meaning that you don't have to worry about the weak ones anymore.
Genius Programming: The game originally shipped without any method of patching it, which proved problematic for a multiplayer game. However, Insomniac managed to patch the game anyway by essentially hijacking the EULA.It must be read to be believed.
Goddamned Bats: The Amoeboids in the sewers at Aquatos. They are everywhere in the tunnels and the bigger Amoeboids will split into smaller ones if you hit them. If enough of them are killed in quick succession (usually when leveling up weapons), the game will slow to a crawl until you leave the sewers.
Also, Angela Cross appears in the cinema audience at the end of the game in her thief disguise. She's later confirmed to be a Lombax, so there's an in-story explanation on why she just didn't appear in her normal attire.
Hilarious in Hindsight: The vid comic narrator expressing utter disbelief at the concept of "robotic pirate ghosts", which end up being the main enemies in Quest For Booty.
Ho Yay: One of the last cutscenes of the game shows Skrunch trying to kiss Clank. The response: "Do not even think about it!"
Moral Event Horizon: While nether Dr. Nefarious nor Klunk cross this line (yet, in the latter's case), Courtney Gears does by betraying the Q-Force, abducting Clank and turning Skidd into a robot. Not only all that, she's a bit too sadistic when Ratchet fights her later on.
Captain Qwark nearly crosses this line when he fakes his death, and cowardly refuses to rejoin the fight. He manages to avoid this line in the end.
That One Side Quest: The Qwark vid-comic time trial skill points can be a pain to get through, as they require precise platforming and dying doesn't restore the lost time, meaning that even one death can fail the challenge.
They Changed It, Now It Sucks: The Hacker segments. In both of the previoustwo games, there was a gadget specifically meant for furthering your progression through a level, either by (literally) unlocking a new area or path or by fixing an electronic device that you needed to use. Whereas the previous games incorporated puzzles into the hacking minigames (Tresspasser, Infiltrator), or at least were over fairly quickly (Electrolyser), using the hacker isn't nearly as interesting or fun; in fact, you may find it to be pretty damn annoying. Even worse, in most instances each Hacker segment has multiple stages, meaning you'll have to beat the mini-game more than once to open most roadblocks.
Tough Act to Follow: Up Your Arsenal is generally considered to be the best game in the franchise, which is why Deadlocked and Size Matters initially didn't do so well (though while Deadlocked eventually became popular in it's own right, Size Matters is hated by a lot of fans for being a Narm Charm and is eventually declared non-canon).
Underused Game Mechanic: The Warp Pad is a gadget that lets you place a location to warp to at select points. There are 2 of these select points in the entirety of the game, which both appear in the same level. Even better, one of the sections can also be completed using the Charge Boots instead.