In episode 7 of the first season when Sousuke, Kurz and Kaname were fleeing in Khanka and a chopper was chasing them. Sousuke promptly threw Kaname high in the air, blew the chopper with a well-thrown knife then turned back and caught her on the way down. Upon realizing that she's out cold, Kurz remarks "Wait 'till she wakes up..."
Episode 8 has Sousuke playing a dating-sim to try and understand the fundamentals of dating/teens in general. It ends with a predictable 'Game Over' screen, but his reaction to it is comedic gold.
Sousuke: Wait! If you cut off negotiations, it can only lead to war! Accept the truce and I'll listen to anything you might have to say! We should work together on a compromise!
In the epilogue of Always Stand By Me, Sousuke and Al have been recovered from Merida by US Marines and are currently being held at Okinawa, pending transport to the continental US. What's left of Uruz Team assembles to break him out... and then before their plan goes into action, Sousuke breaks himself and Al's computer box out of the base, and swaps cars with the rescue team, heading to Tokyo. Everyone stands still, dumbfounded... before remembering that they have to get lost now, as angry Marines start chasing them. Al requests for a new body, and Wraith angrily berates him, saying there's no budget, prompting Al's next request:
Al: In that case, please install me in a Trans-Am.
At the end of Kaname and Sousuke's haircut scene, to prevent herself from kissing Sousuke while he was sleeping, Kaname shoves his head under the tap. "Well, then I'll wash your hair!"
In the final episode of The Second Raid, Sousuke plays the straight man to his own mecha. They both agree the mecha is the funnier of the two.
And of course in the same episode where Kaname was about to dramatically enter the stage but Sousuke supposedly screwed it up by saying "Chidori, you're alive?!" Cue to her beating him up real good.
Most of Gates lines apply, but I especially favor, "I wasn't planning on killing any Mithril today, but shit happens."
Then during Sousuke's killing of Gates, everyone else is watching the resulting light show with some measure of shock and awe... except for Kurz, who's grinning at the awesomeness. And we can't blame him.
the Full Metal Panic!: The Second Raid OVA is full of them:
The part when a half-asleep half-naked Tessa wanders in on Sousuke while he's running an AS combat simulation with Al and mistakenly thinks she's still asleep and having an Erotic Dream. Sousuke freaks out.
The best part is Al's comments.
Al: A new and high-threat target is approaching. The situation is disadvantageous. (Glomp!) Damage to the chest. The situation is dangerous. (wakes up completely) Enemy behavior has developed abnormalities. (runs away babbling) Enemy has retreated. You’re losing the chance to pursue.
Melissa programs the mecha AI's for...
When it fails, Tessa told her not to worry about it right before slapping her and the technicians with a pay cut, and damage reports by the next day.
Kalinin making borscht that requires very precise timing, and includes ingredients like cocoa powder and miso. It was a memento of his dearly departed wife and was so bad Tessa wondered if it's actually a dish she served up as revenge for him being away so much...
An episode of the anime that Lt. Clouseaux was watching featured a Underwater Kiss... until Kurz got a hold of them and replaced them with footage of two pigs kissing. Clouseaux was NOT amused.
The fact that Clouseaux watched anime and was adamant about keeping it a secret is pretty funny too. When Tessa jokingly told him to stop, his reaction made it look like he was being tortured.
Mardukas shows up to stop them fighting and what follows is an hours long lecture. It gets better when Tessa somehow ends up listening with the guys, and they had no idea how that happened.