These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
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.
Ensemble Darkhorse: Dr. Nefarious & Lawerence, to the point that Quest For Booty seemingly exists just to anounce their return as the BigBads in A Crack In Time, and Nefarious became a playable character in All 4 One.
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.
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 have 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.
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.