The reveal in "Treasures of the Tonga Trench", in which the precious glowing "gemstones" the crew discovered turn out to be the feces of a giant bioluminescent sea creature. So funny that its practically the only thing I remember from the show.
Pretty much any of Krieg's wacky schemes, for that matter.
This gem from the pilot:
Krieg: What the... these are all family films! I told you to get something interesting! Look... this is a submarine. Can you say that?
Krieg: Good! This is not a monastery! [sigh] Forget it, I'll pull something from my personal library.
On launching a "magma buoy" into a volcanic vent: "Oh, I think I'll pass. I doubt Raleigh or his ceramic suppository require my presence."
In Vapors, Lucas explains money to Darwin. Darwin, who finds the entire concept of paying for fish when he can just go catch some to be completely ridiculous, says, "That sucks." For Darwin, this is a glorious Precision F-Strike. Later, Darwin refuses to help Bridger set up some party lights unless he gets paid, at which point Bridger throws up his hands and declares he'll do it himself.