I'm going to have to throw MGS3 into the ring here:
Sigint: Snake, what's up? Why are you naked? I know there's a "NAKED" option under "UNIFORM" that lets you take off the upper part of your uniform. But without a shirt on, your camouflage sucks, and your stamina goes down faster. You don't get any advantages whatsoever.
Naked Snake: Sure there are.
Sigint: Like what?
Naked Snake: It feels good.
Sigint: ...Man, you do whatever you want.
Naked Snake: I will, thanks. Just one question, though.
Sigint: What?
Naked Snake: Is there a way to take off my pants?
Sigint: Say what?
Naked Snake: My pants, can I...
Sigint: Aw, hell no! This FOX unit is a nut fest!
Colonel Campbell: [after "accidentally" killing Ocelot] Snake, what have you done? You've changed history. You've created a Time Paradox!
Sigint: [regarding the Soviet camo] Looks like Soviet guards will hesitate to attack you from behind with this on.
Naked Snake: You mean it has advantages, other than being stylish?
Para-Medic: [On the radio] Snake, have you seen "007: From Russia with Love"?
Naked Snake: I don't like those movie. Real spies are nothing like James Bond. It's pure fantasy.
Para-Medic: Snake, I don't think the Major's going to like you saying that.
Naked Snake: And even though it's fiction. I can't help but comparing myself to Bond.
Major Zero: What exactly don't you like about James Bond? Is it the fantastic gadgets? The cars? The guns?
Naked Snake: Major...!
Major Zero: Snake, wouldn't you like to have a gun shaped like a pen?
Naked Snake: What good is a pen going to do me in the jungle? I'd look like a fool.
Major Zero: Then what about a snake-shaped gun? You could make it look like you're grappling with a giant snake and then get a shot in on the enemy while they're distracted.
Naked Snake: Ok, now you're being ridiculous.
Sigint: [if you call Sigint while wearing a cardboard box] Uh,Snake... what are you doing?
Naked Snake: I'm in a box.
Sigint: A cardboard box? Why are you...?
Naked Snake: I dunno. I was just looking at it, and suddenly I got this irresistible urge to get inside. No not just an urge - more than that. It was my destiny to be here; in the box.
Sigint: Destiny...?
Naked Snake: Yeah. And then when I put it on, I suddenly got this feeling of inner peace. I can't put it into words. I feel... safe. Like this is where I was meant to be. Like I'd found the key to true happiness.
Sigint: ...
Naked Snake: Does any of that make sense?
Sigint: Not even a little.
Naked Snake: You should come inside the box... Then you'll know what I mean.
Sigint: Man. I don't wanna know what you mean! Between you and Para-Medic, is everyone but me that is hooked up with the Major strange?
Naked Snake: ...
Sigint: Yeah, well, anyway. I suppose even that dumbass box might make a decent disguise if you wear it inside a building.
Sigint: From the looks of it, it's fitted with a 100-round drum magazine... and it never runs out of ammo?
Naked Snake: Never.
Sigint: Why's that?
Naked Snake: Because the internal feed mechanism is shaped like an infinity symbol.
Sigint: Ah, I get it. Yep, that'll give you unlimited ammo.
Dammit...I can't find a transcript of the hilarious one about the glowcap mushrooms.