During a codec conversation with a female character if you press R1 to have Raiden's positive thoughts he will think how cute they are. If Rose is angry at him or something like a negative thought would be "You're a real egoistical woman."
"WE MANAGED TO AVOID DROWNING", yes it's Narm - but it is fucking hysterical, especially Raiden's delivery.
"There's a terminal near the elevator: a node." "Did you say 'nerd'?" "Not nerd, node." "Oh."
Raiden: Pliskin, I saw someone wearing a cardboard box just now...? Pliskin: A box? I don't know anything about that. You sure you weren't imagining things? Raiden: Of course I'm sure. Do you think it's one of the members of Dead Cell? Pliskin: How should I know? Raiden: I don't want to fight someone like that. Pliskin: Why not? Raiden: Because it looks so dumb. Anyone who's willing to be seen like that must be completely insane. I mean, he's a psycho; there's no question about it. Pliskin: Um, yeah...
Later, when you get the box, Snake goes on a tirade about how the cardboard box is the most essential and useful tool in an infiltration mission.
Pliskin: Look, I'm not exaggerating when I say the success of your mission hinges on how you use that cardboard box.
If you listen to Raiden carefully, it sounds like he regrets dissing it earlier.
Also, if you ruin his box, he'll get angry at Raiden for ruining it. "You know I've lost a couple, thanks to you."
If you listen to Emma at the right moment, you can hear her talking to herself about Raiden, saying that he's "easy on the eyes", but that she's weirded out by his hair. Have a codec call with her right afterwards, and Raiden will confirm that his hair is in fact not a wig.
Add one of the actual wigs you can unlock in the game and it's funnier.
It's actually possible to get peed on at one point. Have a codec call right afterwards, and Campbell will apologize. Then Rose will say that it's ok, but that Raiden has to promise to take a shower as soon as he gets back.
Colonel: Ugh...Raiden, my sympathies. Sneaking missions are called "wetworks" for a reason.
And before that, there's a short cutscene of the guard in question's Potty Emergency:
Guard: Oh! I'm going to go in my pants...no one's looking, right?
The Colonel's "conversation" with you if you snap a pic of Jennifer's underwear.
Use the directional microphone on E.E. when she's crossing the struts, then call her after that. After that, she runs into Johnny Sasaki and Hilarity Ensues. Also, try shooting the cardboard box that you see between the struts, using the codec when you're in the bathroom, messing with the projectors in the Tanker, talking to Otacon (and later Snake) about Pentazemin to cure seasickness, etc.
Johnny: "Stay away from good-looking women when you're fighting. Otherwise you'll get hit with diarrhea."
If you point the microphone at Snake, he contemplates whether he should ask for Otacon's okay to date Emma.
Particular mention to Otacon reading Chineseproverbs. He's trying to motivate Snake like Mei Ling did, but it becomes quickly obvious that not only has Otacon never looked at the proverbs before the calls, he also has no idea what they actually mean.
From Substance, there's the Snake Tale "External Gazer", which already has a Mind Screw plot about mythical sea monsters and virtual reality missions before the kicker: forcing Snake to play as Raiden as Cool and Unusual Punishment, with his only hope of survival being to Rage Quit.
If you get caught while sneaking around naked in Arsenal Gear, you can run back to the interrogation room and pretend that Raiden is still shackled. Any guards that follow you in will dismiss the alert, but not before staring and muttering that they "wish I had that...".
The recap section tells us of the investigator Gary McGolden, and his research into Shadow Moses. However, his exploits are completely hilarious, including swimming 20 miles in an arctic ocean disguised a giant tuna, and the implication that he actually ended up on a different island without realizing it.
Using the camera to take photos of the more fanservicey things results in Otacon chiding you for doing it, while making a back up of them, just in case. Also, if you take a picture of a certain image, Otacon comments that it "explains a lot".
This, along with the Codec calls from when Raiden is in the various bathrooms, are found in this video. The best one is Pliskin being fine with it, saying "anything goes".
Getting caught in one of the rooms full of Marines.
Especially if it's by using the projectors.
There's also a random chance that one or more of them won't be wearing pants.
Calling Snake when he's knocked out or asleep.
Try to shoot Snake while he's sleeping.
If you're on a playthrough where Snake and Raiden are wearing sunglasses, it's really hard to take any scene seriously.
When Raiden asks Plisken about Vamp, we get a several minutes long retelling of Vamp's tragic backstory, including how as a child he was the only survivor of a terrorist bombing and lived for several days by drinking the blood from his family's dead bodies. Raiden asks if that's how Vamp got his codename, and Plisken says, "No, it's because he's bisexual," leaving both Raiden and the player to have a moment of WTF.
This moment, where Raiden, in a Codec conversation with Otacon, gets pissed about Snake and trash talks him. Not realizing, of course, that Snake is right next to Otacon and can hear every word. What makes it even better is that as soon as Otacon reveals that fact, the Codec switches to Snake, perfectly silent, with a Death Glare on his face.
Otacon: Ha ha. You know, you're a pretty interesting guy. You're just like Snake said. Raiden: ...What did he say? Otacon:That you're a weak, simple-minded, stubborn fool. Raiden: A-a weak, simple-minded... Otacon:Ah, don't worry, he didn't mean anything bad by it. Raiden: "Nothing bad"? What could possibly be worse than that? That lying, useless, backstabbing, mincing son of a — Otacon: Raiden, I'm his friend. I know him better than anyone else. I know he's not that kind of guy. Raiden: Yeah? So what? Otacon: And, by the way... there's one more thing you should probably know about Snake. Raiden: What? Otacon:He's right here. Raiden: ...Next to you? Otacon: Yep. Raiden: Did he hear.... Otacon: Every word. Snake: ... Raiden: I'm, uh...I'm just gonna get back to the mission right now.
Pressing R1 or R2 during a Codec sequence plays a brief audio snippet of Snake/Raiden's thoughts on the current matter, with R1 being a positive and R2 being a negative. They're random but the funniest to get is Raiden's "Whatever!" upon hitting R2. Players could make a game out of pressing the R2 button as Raiden, and upon hearing him shout "Whatever!", immediately skip that entire Codec sequence.
Escorting Emma can be a pain in the butt and the Colonel can suggest that you knock her out to drag her through the sea lice (or any other dangers that lie ahead) Using the M9 to put Emma to sleep is an obvious choice, but you can also knock her unconscious by punching her. Pistol whipping works too, even if you use the huge and heavy Nakita missile launcher; one swing is enough to knock the poor girl out.