Motoko's initial confusion with Logicoma and her exasperation when she deduces that it's an old model after seeing it use signal lights was pretty funny in its own right.
border 2: Ghost Whispers
After surviving the highway shootout with Batou, the Major asks the Logicoma for more ammo. The Logicoma opens its storage trunk, only to reveal it's empty.
Motoko: "Why the hell are you empty?"
Logicoma: "They thought I was hacked, remember?!"
Aramaki comes up with a last ditch plan to halt Soga's hack on Pandora by ordering the city's Transportation Ministry to activate the hundreds of automated roadblocks on the highway and road system, bringing all traffic in one of the world's largest metropolises to a halt.
Aramaki: "My apologies to the ministry: I'm about to cause the worst gridlock anyone's seen in 30 years."
What makes it even funnier, is that Batou doesn't drop the smart-ass grin until after he's raised his fist and right before he slugs himself, he evidently doesn't realize there's anything weird in what he's doing.
After Batou confirms the Qhardi terrorists are likely going to be targeting water infrastructure facilities, Saitou identifies 78 possible locations that fit that description in the city. To Ishikawa's chagrin, the Major orders him to check them. All of them.
Ishikawa: "Damn. You know, intelligence subcontracting pays a lot better for half the work!"
Early in the OVA, everyone is discussing the difficulty of supporting their prosthetic needs, talking about the Major's unsuccessful love life while also remarking that a Section 9 op isn't exactly a job for someone with a relationship. By the end of the episode, just as the Major extends an invitation to the non-cyborg Togusa, he gets a call from his wife that she's about to give birth. The Major is stunned.
Just the fact that as she's in the middle of offering Togusa a spot on the team, he suddenly cuts her off to answer his phone and immediately begins spazzing out, jogging in place out of raw excitement while she stares at him, gobsmacked.
During the flashback to how Motoko and her boyfriend first met, she holds up her prosthetic hand, contemplating it, and he walks up and takes it in his. The face she makes in response to his forwardness can only be described as being an Angry What.
border 4: Ghost Stand Alone
Motoko stripping the clothes of Batou's virtual avatar in the middle of one of their meetings with the entire team for suggesting that he should lead the team instead.
And immediately afterward, when he challenges her to a fist fight in the real world, she then proceeds to slug him hard enough in the face that it knocks him down and leaves a very large bruise.
A Logicoma comes to the rescue, shielding The Major from enemy gunfire and ejecting Batou from the passenger pod they finally managed to get installed in the things, sparing the team from the continued indignity of having to cling onto the exterior for dear life.
Something about the sight of three Logicomas dogpiling on a much bigger spider tank, and having neglible success in subduing it before getting tossed off and sent fleeing for cover.