The Cavil hiding out with the Resistance on Caprica returns to Galactica, and since they already have a Cavil he's revealed as a Cylon. As that Cavil is arrested: "Would you mind telling me what's going on? I am not a frakking Cylon! I'm not... (sees the other Cavil in the cell) Oh. Well. Okay, then."
Earlier in the same episode when Tyrol first figures out that Cavil's a Cylon and tackles him. After Tyrol gets up, Adama has every gun present pointed at the Cylon, prompting Cavil to quip, "Well, this is an awkward moment."
Any time Cavil threatens Baltar. For instance, when discussing how the Cylons need to instill a little fear in the people of New Caprica:
Cavil: "I know: let's execute Baltar."
And then in "The Eye of Jupiter":
D'Anna: "You give us the Eye of Jupiter, we'll let you go."
Cavil: "And...we'll throw in Baltar."
Baltar: "What are you talking about now?"
Felix: "Got any porn in there?"
pretty much any moment with Baltar and Head!Six (i.e., the Six that only he can see)
After Gaeta perjures himself in Baltar's trial, he angrily brings up the time that Gaeta had tried to kill him with a pen: "The whole fleet knows this man tried to stab me through the neck — and you missed! Butterfingers!"
The best part? That was an ad-lib from James Callis.
Felix to Starbuck: "I guess a pity frak is out of the question then?"
This was also an ad-lib!
The entirety of Baltar's introduction to Head!Baltar, starting with his conversation with Tory.
Tory—I came here on my own.
Baltar—::with a perfectly straight face:: And I slept with your boss last night.
The whole dinner scene is hilarious, including Roslin's totally un-subtle passive aggressive hints that Ellen is a cylon, but this moment might be the best:
Adama: Which means—any one of us could be a cylon.
Ellen: BOO! (Everyone jumps about a foot in the air.)
It's a small moment, but the way Roslin hands Ellen the bottle of booze as she's leaving. Roslin doesn't even bother with her aforementioned un-subtle passive-aggressiveness and says nothing, having only a comically blank expression on her face as she moves the minimum amount to accomplish the task. She comes across as less "tired" and more "completely given up all hope of sanity."
And the scene after dinner where Lee, Adama, and Roslin can't seem to figure out if it'd be better or worse if Ellen turns out not to be a Cylon.
The other scene after dinner with Saul and Ellen, completely blitzed, trying to make their way back to their quarters. It starts with Ellen making fun of Adama for being a stick in the mud; "He's one of those faces on a totem pole." This quickly devolves into Ellen (correctly) realizing that Adama's claim of being on course for Earth is completely made up to give the survivors something to look forward to, which she expresses by bouncing on Saul's shoulders while loudly sing-songing that Adama has no idea where Earth is. Even Ron Moore can't handle it during his commentary, where he has to apologize for losing his train of thought on account of the scene.
Starbuck walking in on Baltar having sex with Head Six under the table...this is the six only he can see.
The entire Gaeta/Baltar bathroom conversation in "Six Degrees of Separation."
Baltar (on the toilet): "So, um... How're you doing?"
Gaeta (on the toilet): "Uhh... Mmm..."
Baltar (still on the toilet): "You're busy, yes, I know, I don't mean to distract you, please, don't let me interrupt." *starts to whistle*
Later, in that same conversation:
Baltar: "So how's it going over there?"
Baltar: "In the lab, that is. I'm talking about the photograph."
A missing ship lands in the hangar to reveal... Ellen Tigh.
Hot Dog: How many dead chicks are out there?
During one of the bleakest episodes of the series so far, the fleet is about to make a dangerous jump through a multiple star system because the only potential source of food within reach is on the other side. Saul Tigh is telling Adama how the starving civilian population is starting to get unruly.
Adama: I hear they're still eating paper. Is that true?
[They both lose all composure and dissolve into laughter for about half a minute.]
Plus this gem from the series finale: "I don't mean to rush you, but you are keeping two civilizations waiting!"
"I'm a friendly, okay. We're all friendlies. So let's just... be friendly."
"I will?!" "You see them?!"
"Bitch took my ride."
Baltar is asking Admiral Adama, President Roslin, and Lee Adama for guns. To which the admiral replies, "You both can listen to this if you want. I'm going to the head note naval term for the bathroom to do something productive. A little project I've been working on."
Starbuck literally drinking Anders under the table.
During the miniseries, Adama's reaction to Roslin's message telling him to rendezvous with Colonial One and help aid the civilian ships.
Adama: Is this a joke?
During "Torn" Helo asks for a callsign for his wife. Cue the Hurricane of Puns. Among the best: "Chromedome!", "Windup Toy", "Micro Chick!" and "Digital Dame".
Colonel Tigh commenting on the primary consequence of destroying the Resurrection Hub: "We blow the hub and billions of skin jobs lose their bath privileges."
The ultrasound scan of Tigh's and Caprica-Six's baby, with this offscreen dialogue:
Six: "I thought I saw it."
Tigh: [annoyed] "Saw what?"
Cottle: "Everyone, shut the frak up for a second."
Cottle: "Try looking with your eyes... eye."
"You know, there are days when I *really hate this job."
"Strength comes from within." *Caprica-Six prompts Baltar. Baltar goes O_O for a bit, then...* "... and from guns! More guns, bigger guns, better guns!"
More from Cavil in the finale, when informed that firing at Boomer will also risk killing Hera. "Feel free to keep stating the perfectly obvious. It fills me with confidence."
Starbuck is stranded on a planet and her only hope is to learn how to fly a Cylon raider that she shot down. The first control she tries turns out to fire its guns, and we cut to her looking completely freaked out and telling herself "Lesson one: don't touch that."
Along with Tyrol deadpanning "Don't shoot anything" when she manages to get the ship working again.
The best of the conversations where Gaius Baltar has to talk to Head Six and a real person at the same time, from Kobol's Last Gleaming, Part I:
Baltar: "I am not a toy! I am not your plaything!"
President Roslin & Head Six, in stereo: "Plaything?"
A minute later, Baltar is washing his face in the lavoratory, and Head-Six appears in the mirror. Baltar tells he he would like to be left alone, if she doesn't mind, and she responds by slamming his face into the mirror.
The Battlestar Wiki entry for New Caprican leaf, aka Fleet Wheat, aka Battlestash Galactiganj.
Gaeta and Dee's shared eye-roll in "Resistance" when they realise that Tigh's been drinking on duty again.
And in a deleted scene from season 3, when the two of them notice that Adama and Roslin are spending too much time together, have a "are you thinking what I'm thinking?" moment, dismiss it as impossible, but can't help but laugh ("that's an image I don't need in my head"), and keep laughing even when they arrive in the presence of a so not amused Saul Tigh.
Roslin pranking everyone into thinking she's going to Christen the newly-built Blackbird old sailing ship style (ie, smashing a champagne bottle on it, a very bad idea with this far more fragile vehicle).
Made even more hilarious when you know that Mary Mc Donnell was having a massive giggle fit the entire time they were shooting the scene.
The moment in "Home: Part 2" when Dr. Cottle asks Baltar to stop moving around in the brain-scanning machine. "Will you stop going crazy in there?" Gaius, wide-eyed and paranoid: "I'm not crazy!!"
Gaeta running verbal rings around a frustrated Starbuck duing the mess hall scene in 'A Disquiet Follows Me Soul', ending with the viciously hilarious diss 'I guess a pity frak's out of the question...'
Baltar arguing metaphysics with Head-Six in "Six Degrees Of Separation."
Baltar: Which leads me to conclude that Cylons are little more than toasters! ....with great-looking legs.
Gaius Baltar trying to calm the Hybrid on the Rebel Basestar while it's making random FTL jumps is just all kinds of hilarious.
Baltar: Shhhh. Shhhh. Hey! Hey, stop jumping the ship!
During 2x03 "Fragged", Baltar points out that Crashdown is clearly crazy to order him to fight in the attack on the Cylons, saying he's never fired a gun in his life. The group's medic points out that she hasn't fired a gun since basic training, and then Baltar glances to Cally, whose response is "I joined to pay for dental school."
Hot Dog, as he's about to be launched in a Viper while Galactica is in freefall in New Caprica's atmosphere:
During 4x18 "Islanded in a Stream of Stars", Baltar is shaving in the bathroom when...
Starbuck: "Missed a spot." *beat* "By your left sideburn."
Starbuck: "The latch was busted."
What makes this extremely funny is that Starbuck's on the toilet during this conversation, reading something.
When Head-Six helps Baltar stand up against the guards that were blocking and attempting to take over his and his religious followers' hideaway. No matter how many times Baltar is beaten to the ground, Head-Six insists that he keeps fighting, and lifts him up from under his arms... Which means in reality, Baltar is rising up from the ground in the most bizzare and peculiar way that could in now way support himself on his own, leaving onlookers bewildered and the guards practially begging him to stay down... All while Baltar is telling Head-Six to leave him on the ground. Uplifting religious sounding music accompanies this, as if to imply his followers believe it is God lending Baltar the strength to keep standing. The ragdoll like movements really adds to the humor.
IT'S IN THE FRAKKING SHIP!
From "Crossroads, Part II"
Baltar (to Lee): "That would be the quickest way to absolve all your responsibility, wash your hands of the whole affair! You get back to your life..."
(to Romo Lampkin, who has a blank look on his face)
"You get back to...whatever it is you do!"
Funny, because the viewers have never seen or heard of Romo before Baltar's trial.
Romo asks for a room with a view if he defends Baltar. A later episode shows the window is ridiculously small, presumably Roslin's payback for him getting Baltar acquitted.
Baltar mistaking Shelly Godfrey (a Six model Cylon) for Head Six, and his reaction when he realized she wasn't Head Six:
Baltar *happy*: "You can all see her!"
Several meta-examples are provided by the commentary tracks:
Ron Moore explaining that Edward Olmos' no-nonsense reaction at a press event to being asked what he thought of backlash from fans of the original series was to respond with "Don't watch it. If you're a fan of the original, just don't watch it, it'll be too painful, turn it off." Moore goes on to say that the reporters were uncharacteristically generous and gave him several chances to backpedal, none of which he took, all while the president of the SyFy channel kept a straight face but clearly wanted to physically yank him out of the room.
Moore's wife admitting that she regularly checked the official forums, prompting Moore to completely freak out at the idea of the forum-goers trying to work his wife into getting her to convince him to do something specific with the show. His wife is referred to as "Mrs. Ron" from then on.
Moore having to wait for Mrs. Ron to leave before he can smoke, which leads into a Running Gag of him insisting that smoking is cool, dammit.