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 are 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.
An episode of the anime that Lt. Clouseaux was watching in the Full Metal Panic!: The Second Raid OVA featured a Underwater Kiss... until Kurz got a hold of them and replaced them with footage of two pigs kissing. Clouseaux was NOT amused.
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.
Also, the entire opening of the 2nd Raid OAV when a half-asleep, half-naked Tessa wanders in on Sousuke while he's running an AS combat simulation with Al and mistakenly think's she's still asleep and having an Erotic Dream. Sousuke panics and Al's comments don't exactly help.
Al: A new and high-threat target is approaching.
Sousuke: (hears something, turns around, sees Tessa, promptly jumps out of chair.) Aaagh!
and later, after Tessa wakes up and runs out of the room in embarrassment...
Sousuke What was that all about?
Al: Enemy has retreated. You are loosing a chance to pursue.
Sousuke: Shut Up!
In Fumoffu, when Tessa briefly attends Jindai High, she shows up to swim class in a School Swimsuit. When Kaname questions it, she explains that Kurz insisted she wear it...and we get a Flash Back to Kurz conducting a full military-style briefing, complete with data screens and a 3D model of a girl in a school swimsuit. The cherry on top is all the male Mithril crew sitting around Tessa who nod solemnly at Kurz's presentation.
Also in Fumoffu, Sousuke is debating what to eat at the popular bakery stand during lunch. Kaname tells him that he should "be assertive" lest there be nothing left. So, Sousuke pulls out his pistol, fires it into the air and demands a plain roll, then causes a panic when he threatens to shoot them. The crowning part is Kaname's reaction: she is shocked not at the fact that his pulled out a deadly weapon at school, but that HE WANTED A PLAIN ROLL.