Eli's running commentary of the Apocalyptic Log in "Time", but particularly.
[In the video, Rush runs off during a fire fight with alien creatures] Video!Eli: Where are you going! You're crazy! He's crazy! [Cut back to the crew watching the video] Eli: [turns to Rush] You are! Rush: [shrugs]
Also in the episode "Earth", in the first glitch with the communication stones. Colonel Young is having sex with his wife, when suddenly he and Telford switch consciousness for a few seconds, right at *ahem* a very important part in the action. When they switch back again, it goes something like this:
In "Divided", the communication stones are used to bring a doctor from Earth. She becomes increasingly mortified by the weird conditions on the ship (alien venom as an anesthetic, a makeshift fiber optic camera made from a hovering camera ball, and the fact that the ship is being attacked). TJ simply responds, "Welcome to Destiny." Hmm, that has a certain ring to it.
Chloe tries to justify having picked up archeology to Colonel Young, with Eli's help.
Counts as an in-universe CMOF, as their rather long and awkward string of justifications ends with Young chuckling to himself once they leave the room.
Later on, Eli claims that he called Greer out for being afraid as a joke. Because he thought that they were on that level in their relationship.
Greer: I'm going to stay up here and cover your backs. Eli: What are you, scared? *Greer gives him a stare* That was a joke. I'm sorry, I must have mistakenly thought we were on that level now. You know, friends who can kid each other like that? *Greer removes shades and switches to a full blown death stare* Please don't kill me?
Same episode, when the away team have to call in a rescue team due to the aftermath of a spider attack, and having to explain it to Young.
Scott: It was a sizable spider, sir.
O'Neill is good for these.
Telford: What makes us so special? O'Neill: I know what makes me special.
Greer vs. Alien Fruit. Both times ("Justice" and "Faith"). The first time, he pretends the "alien sweet potato" tastes delicious ( which was a little too generous). The second time, he eats a completely random fruit to the horror of the rest of the off-world team.
TJ: We don't even know if it's poisonous! Greer: (deadpan) We will.
Greer vs. Alien Wildlife. "Is it something we can barbecue?"
Then again, in "The Hunt": Greer and Varro are carrying a wounded corporal back to the gate. They suddenly see a "space deer". Next scene: "Becker's Barbecue" on Destiny.
Eli and Young's exchange about the returning crew members' explanation in "Visitation."
Eli: "Any sufficiently advanced technology is indistinguishable from magic." -Arthur C. Clarke Young: "Turn the mic back on." -Winston Churchill
Apparently, Young starts to get how to make Eli understand what he wants (from "Resurgence"):
Young: (about how Eli should send a signal to an alien ship) "Ancient, English, Bat-Signal, and whatever else you've got."
Volker on seeing the alien ship in "The Greater Good"
Volker: (deadpan) "New friends. Yay."
In a later episode, when Rush dryly comments on their status, Brody joins in:
Rush: Well at least we have a full tank of gas.
*Sarcastically in unison*
Volker / Brody: Yaaaay.
The Kino mini-episodes can be full of funny:
"We... turned him purple."
Eli taking a Kino on a tour of the ship and getting lost.
Eli: And this room is... *looks around in confusion* I don't think I've been in here before... *wanders off camera*
Scott catching people watching South Park when they should be exercising, and how they get him to go away:
Scott: [About running two miles] I can do it under 23 minutes.
Eli: Really? Funny, because there's a protein bar here that says you can't.
[Scott runs off, everyone goes back to watchingSouth Park]
Doubles as Getting Crap Past the Radar: Eli is discussing food with Camille and Chloe and they mention "purple fruits" with enthusiasm. Eli's confused because the fruits tasted bad. Chloe and Camille trade sly grins that indicate they weren't talking about eating them.
Rodney McKay is invited aboard to peer review Eli's extremely complicated science-y plan. After leaving them alone for a little while, the crew comes in to check on their progress, finding them heatedly arguing over equations they'd written on the wall. After some prompting, they learn that Eli and Rodney had long ago finished checking it over and determining that, yes, the plan will work, and ever since they had been arguing over finer points of mathematical theory and wormhole physics. The best part is that the two of them have clearly been having the time of their lives doing this.