In the beginning of the game, Ratchet and Qwark are flying through space looking for Clank, and Qwark decides to monologue about the adventure, placing heavy emphasis on the fact that Ratchet's alone. Ratchet promptly reminds Qwark that the ship has an ejection function, with a tone that explicitly states he's about five seconds from using it on Qwark if he doesn't shut up.
And, of course, there's the crashing sequence that follows that. It starts with Qwark panicking and referencing the old "Always wear clean underwear, because you never know what's going to happen" thing, and ends with...
Ratchet: (looking around in the time rift) Whoa.
Qwark: I know. (Beat) So much for clean underwear.
The best part is, without a doubt, the face that Ratchet makes after Qwark says that. Someone get that lombax some Brain Bleach...
After saving the fongoids on planet Zanifar, you hear this exchange:
Fongoid: Boy, I can't wait to get home and see my wife!
Fongoid #2: Yeah! Me too!
Another one from the Fongoids.
Fongoid: My brother is still stuck on the oil derrick. He's kind of a jerk, but we should probably still save him.
Everything said by Dr. Nefarious in this game. Large Ham at its absolute finest, catapulting him straight to Ensemble Darkhorse status... If he didn't already have it.
Becomes even funnier when you realise that the Valkyries would have had access to warp technology that would enable them to make the journey in minutes. A trip that should have only taken minutes lasted decades. Epic. FAIL.
Qwark finds out that the Agorians aren't on the best of terms with Nefarious. Logic dictates that would mean they would want to ally with him and Ratchet who are against Nefarious, so he goes off on his own to recruit them. Then he calls Ratchet to give him an update:
Ratchet: I read you Qwark. How are things with the Agorians?
Qwark: Ehhhh... not so good. Somehow they got the impression I'm some thrill seeking warrior with a thirst for battle!
Ratchet: Well, did you tell them you're a thrill seeking warrior with a thirst for battle?