Pretty much every conversation between Pox and Crypto.
Pox: If we want this invasion to run smoothly, we must identify the dominant lifeforms on this world. Those "Lactating Bovoids" are likely candidates. Crypto: Surely you don't mean those fowl-smelling gas bags beyond the fence? Pox: Yes, I'm afraid I do. Crypto: But they're covered in nipples! Pox: NOW Cryptosporidium!
In the mission "Furon Down", Crypto is captured and awaiting autopsy when the Mad Scientist assigned to the job bursts out with this hillarious rant:
You call zis a scalpel? I vouldn't cut cheese mit a knife zis dull! Und ze rust... Gott in Himmel! Vat am I, a Bavarian butcher? Zis is an alien cadaver ve're dissecting, not a briskit! I need instruments I can vork vith, or zis little bugger von't be fit for a Hasenpfeffer, much less an autopsy! Go on, you heard me... and buy a decent suit vhile you're at it! Idiot.
In one mission, you must hologuise yourself as the mayor of Rockwell to tell the townsfolk that there's nothing bad going on. The voice, akin to Mayor Quimby from The Simpsons, is just hilarious when the player purposefully picks the wrong choices to say. Like, say, "Insult Audience"...
I gotta tell ya, I've seen some pretty disgusting creatures in my day, but you monkeys take the cake! In fact, all you monkeys is an insult to monkeys! how you became the dominant species of the earth is a total freakin' mystery!
And "Enslave Populace"...
Er, um... BOW DOWN BEFORE CRYPTO! (beat) What, do I have to draw you a picture?
And once one of the people asks you what that has to do with the destruction of the fairgrounds from the previous mission, you can pick "Tell The Truth"...
And finally, when a female member asks why no one in Santa Modesta has experienced anything like this, pick "Feign Ignorance".
How the Hell should I know?!
If you pick "Reassure Audience" instead...
Santa Modesta is experiencing the same problems we are; the difference is, we have that award-winning city desk over at the Rockwell Gazette, and nothing gets past those guys! They keep ME honest!
Pox's reaction to the presidential motorcade being full of heavily armed Majestic Agents.
Look out! It's an ambush! Circle the wagons! Throw me a shotgun! Get the womenfolk inside! Oh... I really must stop watching human television. Oh screw it... DESTROY THEM ALL!
Pox: Crypto! The human senators are meeting today to choose a new President. You must eliminate them. Crypto: Doesn't the Vice-President take over if the President dies? Pox: JUST SHUT UP AND KILL THOSE SENATORS!
Some of the thoughts are just plain hilarious:
If my kitchen isn't the cleanest and shiniest in town, I'll crush ANYONE who disagrees with me... with my dainty manicured fist!
In the sequel, Crypto's bodysnatched a Cosmonaut on the moon to influence the Russians into rebelling against the Blisk aliens. This also becomes a Crowning Moment Of Awesome when Crypto FINALLY comes up with the perfect excuse for why the monsters should be killed:
...THEY'RE TAKING AWAY YOUR VODKA!
In 2, one of your side missions must be carried out while your disciple Shama Lamma is advertising your cult on a radio station. If you screw up, he ends the broadcast with this:
And lastly, I'd like to thank Cryptosporadium, for being a FRICKING IDIOT!
Path of the Furon is funny as hell. A notable example coming from Crypto and Pox discussing this new idea about 'video games.' Pox dismissed Mario, Sonic and Halo as ridiculous ideas, and then, being the genius that he is, suggests that they should make games based on popular movies. What could go wrong?
At the start of the last stage of Path Of The Furon, Crypto destroys a large red forcefield blocking his path with the Saucer's Death Ray. It is immediately replaced by a similar, green one.
Pox: We'll need to think of something else; you can't just shoot this one, because its green.
Before accepting the mission "They Shoot Hippies, Don't They?", if you choose to recap the goal, this conversation occurs.
Crypto: Alright, hit me again with the part about Bongwater's blimps.
The Freak: What?
Crypto: Bongwater. He has blimps full of Revelade.
The Freak: He does? Far out!
Crypto: No- you're the one who said so! You just said he's going to cover Bay City in Revelade gas!
The Freak: Whoa...really? I said that?
Crypto: Focus, Freak! Does he or doesn't he?
The Freak: Does who what?
Crypto: Does Bongwater have Revelade blimps preparing to attack Bay City?!
The Freak: BONGWATER HAS REVELADE BLIMPS PREPARING TO ATTACK BAY CITY?!
Crypto: ...see, kids? This is why you shouldn't do drugs.
In Destroy All Humans 2 in the mission briefing for Kojiras mission:
Pox: I'm picking up a signal in the ocean to the south.
Crypto: Yeah? What kind of signal?
Pox: A radiation signature, emanating in gamma waves from the creature's tortured brain.
Pox: Yes. It's as if the monster is crying out, "Kill me! Kill me!"
Crypto: That's gotta be the most pathetic thing I ever heard. So, you want me to hunt down this monstrosity and put it out of its misery?
Pox: Actually, I want you to read its mind and enter it the source of its cognitive distress, so we can get it some help and over time teach it confidence and self-esteem.
Crypto: ...you've got to be kidding me.
Pox: OF COURSE I AM, YOU MUTATION! NOW GO KILL THAT THING!