Everything to do with the Digital Conveyor, everything.
Jason: What? What was that? Alexander: Uh, nothing. Jason: I heard some squealing or something. Gwen: Oh, no. Everything's fine. Teb: But the animal is inside out. [All the humans in the Conveyor room glare at Teb] Jason: I heard that! It turned inside out? (BOOM!) Teb:[not moving despite being covered in Ludicrous Gibs]And it exploded. Jason: It turned inside out, and then it exploded? Gwen: Hold, please...
Jason trying to prevent Alex from abandoning the convention at the beginning of the film.
Alexander: You're just going to have to figure out what it wants. What is its motivation?
Jason: It's a rock monster. It doesn't have motivation!
Alexander: See, that's your problem, Jason. You were never serious about the craft.
When they've landed the shuttle, and Guy is at the height of his nervous breakdown while Fred goes to open the door:
Guy: Wait, don't open that! It's an alien planet! Is there air? You don't know! [inhales loudly and holds his breath] Fred: [sniffs a few times, exhales] Seems okay.
Guy's breakdown itself, in which he appears to forget that he actually does have a last name:
Jason: You're not gonna die on the planet, Guy. Guy: I'm not? Then what's my last name? Jason: It's, uh, uh - -I don't know. Guy: Nobody knows. Do you know why? Because my character isn't important enough for a last name, because I'm gonna die five minutes in. Gwen: Guy, you have a last name. Guy:DO I?! DO I?! For all you know, I'm "Crewman Number Six"! [Breaks down weeping] Mommy... mommy... Alexander:Are we there yet?
When the cast is first being shown around the ship:
Mathesar: The medical quarters are to the left... Tommy: What the hell is going on?!!? Alexander: Jason, what have you gotten us into? Gwen: I don't believe this, it's insane. Fred: Wow, the floors are so clean.
Especially funny given the 'screensaver' on the Special Features screen, of a Thermian sweeping and then licking a floor. Okay, he licks a finger that he rubbed on it, but essentially the same.
When the actors are first trying to explain that Galaxy Quest was just a show.
Gwen: I mean, surely you don't think Gilligan's Island is— [chorus of mournful exclamations from the Thermians] Mathasar: Those poor people.
Fred's whole personality, especially given his later series.
Clearing out the control room:
Fred: Besides, [cackles] I just had an interesting idea. Guy: Are you stoned? [cue rock monster] Fred:[watching Gorignak whaling on the alien goons with a beatific smile, one arm around Guy and one around his girlfriend, with identical expressions] It's the simple things in life you treasure.
Guy's reaction to Fred and Lailari's, er... public display of affection: "Oh! That'snot right."
On the way out of the spacedock, Laredo manages to scrape theentire ship against the side of the docking bay. Everyone on the bridge cringes as an almighty "EEEEEEEE" echoes through the hull.
Also, after uber-fan Brandon has spent a solid 30 seconds explaining how he realized it was only a show, and the whole thing was fiction...
Jason: Brandon, Brandon! ...it's all real. Brandon: Oh, my God! I Knew It!
Then there was the aftermath where Chen got the engineering crew to group hug.
This takes place during the climax of the film when Sarris transports to the ship and starts killing off the crew, forcing Jason to activate the Omega 13. The camera makes a point of showing a close-up of the faces of all the main characters who get shot, and that the Earth is getting very big in the window: chilling stuff. But then, right before Jason pushes the Big Red Button to set off the potential universe-ending bomb, the camera shows Guy right in the middle of the line of fire, still alive... after he's been complaining the whole movie about the fact that he's doomed. Plucky Comic Relief indeed!
When the crew are first beamed aboard the ship, every one of them is completely frozen in horror at what just happened. Except for Fred, who doesn't seem to be the slightest bit traumatized by the experience.
"That was a helluva thing."
Just before that is Guy's Delayed Reaction to being surrounded by the Thermians in their other, more alien forms.
A Thermian: Our most sincere apologies. We forgot about our appearance generators. Jason: You guys came! Who wants the grand tour? Guy: AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAHHHHHHHHHHHHHHHHHHHHHHHHHH!!!!! ....ahhh! Jason: ...anyone else?
Even funnier is the moment Guy screams above, Gwen nearly jumps out of her skin. Probably an over-reaction from the trip through the black hole, but still hilarious.
Gwen: "My TV Guide interview was six paragraphs about my boobs, and how they fit into my suit!"
Sigourney Weaver playing a bimbo is one big CMOF in itself.
After Jason barks out a series of orders to the crew and insults to the bad guy Saris, including "he's as stupid as he is ugly" while Gwen is busy trying to get his attention...
Jason: Gwen, put me back on with Sarris. Gwen: That's what I've been trying to tell you, you are on with Sarris. Sarris: Perhaps I am not as stupid as I am ugly, commander. Jason: [to Gwen] I gave you the 'kill' gesture. Gwen: No, you gave me the 'we're dead' signal. I was agreeing with you. Like I know where the hold button is.
After everyone telling Guy he isn't going to die on the mining planet. The moment the children aliens kill one of their own, Gwen gets this golden line: "Let's go before one of those things kills Guy!"
And within a minute after Guy hears that line, the team starts thinking up a plan.... Like, oh, how about that one they did on episode 81? Guy turns white and interrupts the group's brainstorming.
Guy: Are we doing episode 81? Jason:[very irritated] It's just a rough plan Guy, what difference does it make if it's episode 81 or not?! Guy: Because I died... ON EPISODE 81!!!!
"Did any of you ever watch the show?!"
Jason and the rock monster: "Go for the mouth or its throat, its vulnerable spots!" "It's a rock, it doesn't have any vulnerable spots!"
And the incomparable:
Guy: I know! You construct a weapon...look around you, can you form some sort of rudimentary lathe...? [promptly dragged away from the communicator] Jason: A lathe?! Get off the line, Guy!!
Brandon gives a geeky, technobabble explanation of what his plans are, and his mother's response is to remind him when dinner is. Once he leaves, she notes to his father, "At least, he's outside." While hilarious, her reaction is more-or-less how most Real Life supportive parents handle their fanchild.