Persona 3: FES gives us the option of going on dates with Elizabeth. This is a woman who apparently only read about the world in books, and the brilliant first date is topped with her pointing out she had asked Igor if she could turn the Velvet Room into a dance club. Also the fountain scenes.
This editor's personal favorite was when you take her to the Shrine. Sliding down the playground's slide without sitting down, getting stuck in the jungle gym...
On an interesting note, Persona 4 has an unlockable song called "Electronica in the Velvet Room", which plays in the Velvet Room and sounds like something you'd hear at a dance club.
"Fortunately, I anticipated this, and brought a good supply of coins...I shall make an opening bid to the fountain spirit of 1 million yen." (proceeds to dump a gigantic bag of coins into the fountain)
And then she realizes there's more than one fountain...
Mitsuru's "execution." Made more apparent in the Drama CD about the protagonist double-timing...
Mitsuru: It's me. EXECUTION! That's all.
Protagonist: W... what!? Why!?
(and after this is the usual tirade relevant about girl pissed off at guy double-timing)
After choosing to talk to Akihiko the night after the aforementioned "execution"
Akihiko: ...I'll say this... The principal offenders were Junpei and Ryoji. We were forced to commit the crime, against our will. We were victims too. ...... ...Now please, do not mention it ever again.
Akihiko, who's usually cool, calm, and collected at all times, even when fighting Shadows, was utterly and totally panicking at the thought of Mitsuru's wrath.
What made this a crowning moment of funny wasn't just the incident itself, but the fact that it practically implied that this had happened to Akihiko before. He had to know that they would be executed somehow.
Combine that with Mitsuru's video. She comments that she should really stop walking around her room without clothes. Did Akihiko forget to knock?
It's even better if you're playing as the female protagonist and let them get away with it while you and Akihiko are lovers. He's so ashamed that he can't even look at you. Ken's response is funny, too. If you're lovers with him, he's upset about what they did, but if you let them get away with it, he has a pretty good idea of what happened anyway.
Not getting caught is just as funny, as Ryoji and Junpei get their just desserts for their perversion anyway: after Akihiko realizes they haven't said anything in a while, he and the MC realize they've passed out from the steam.
This line from Junpei (even better with Vic Mignogna voice acting)
Junpei: I'll never forget Kyoto... How could I, after last night...
Aigis' line back at the dorm if you fail is fantastic: "Commencing ignore mode."
If you catch the boys, she has another one after Mitsuru announces execution: "It was nice knowing you."
Every time Junpei calls Yukari "Yuka-tan," especially the enthusiasm he puts behind it.
"Junpei's Believe It... Or Don't". Apparently he carries a flashlight for the express purpose of spooky-facing.
Almost everything Junpei does or says is a Crowning Moment Of Funny. One notable example is when Yukari goes on a ghost investigation after Junpei starts talking about them.
Junpei: I always thought these stories were fake. But, she seems to be doing research on them. Is it the power of the Junpei Zone?
Yukari: Huh!? What did you just say!?
Junpei: Oh shit... I pissed her off...
And then when you talk to Yukari after he made that comment...
Yukari: Ugh... I wonder why I said that... Yeah, it's Junpei's fault...! Everything's his fault...! The Junpei Zone!? Psh! You really are dumber than you look!
Talk to Junpei the night after Koromaru joins, and you get this:
Koromaru apparently tries to say something after this. It may be... for the best that Aigis isn't there to translate.
Talk to Junpei in the dorm lounge on April 29th:
Junpei: No one's back yet, and we have school in the morning. We probably shouldn't go to Tartarus tonight. Protagonist: No, we're going. Junpei: Listen to me, man. We shouldn't go tonight. Besides, it would be just you and me there. You know, like, Brokeback Tartarus. ...So just forget about it.
The trip to Yasoinaba in Portable is just hilarious, especially with Yuko and Kazushi bickering like an old married couple through the latter half.
A scene that never fails to crack me up is Operation Babe Hunt.
During Operation Babe Hunt, you get appointed as team leader and the music unique to the first full moon boss starts playing.
You then get dragged into being wingman first to Junpei, then Akihiko. Via dialogue responses, you can choose to play along, or go the Deadpan Snarker route. One of the responses you get when the first "target" asks what you're doing is particularly good:
Cleaning up after the (cancelled) school festival in P3P as the girl. Turns out that one of the cancelled events was... a cross-dressing pageant. Junpei, Kenji and Kazushi then start arguing about who would look the cutest while cross-dressing. Then Aigis joins in...
The male scene in FES isn't half bad either. It consists of MC and Kenji preforming a comedy duo act, Kenji borrowing Yukari's nickname for Junpei (Stupei), Kenji teasing Kaz about a possible crush on Yukari, Aigis commenting on Junpei liking maids, and the main event: Yukari, Yuko and Chihiro all converging, while the latter two start blathering on about how much they love spending time with the MC as the 'atmoshere becomes oppressive.' In the end, it takes the combined efforts of Junpei, Kaz and Kenji to save you from a Nice Boat ending as they distract the three girls for you.
Further on the maid thing, Kaz asks what a maid is. For some reason how Junpei says "A pure soul!" with a stunned expression always makes me laugh.
On a meta level and considering that the extended skit with the girls is only triggered if their Social Links are high enough, the whole thing can be considered a joke on the player who probably first thought that the scene would end with a few reversed/broken S.Links.
The ending to the Hermit Social Link in FES. "Maya" totally freaks.
The end of the Devil S-Link consists of Tanaka singing about how he knows he's a Jerk Ass and has no intention of changing his ways. He then faxes the news station just to drive home his point. Courtesy link.
The end of the Hanged Man S-Link in the female route: Maiko mentions in a letter that she really hopes to become family with the heroine, so her dad's idea of making that come true is to ask the heroine out.
Pretty much all of the video recordings will get at least a chuckle out of you, from Mitsuru mistakingly beleiving Fuuka's is having alone time, to Yukari in her maid outfit, a lot of embarrassing things happen.
The very first one will have you laughing (in bemused derision) at Shuji Ikutsuki cracking puns so painfully bad angels fall out of the sky and die on the spot while bleeding from the ears from the sheer lameness of his jokes.
Any of Mitsuru's Fish out of Water moments are funny as hell, such as the one when she thought Junpei was kidnapped.
Officer Kurosawa's reaction really makes that one: "Well, son, looks like you've got a death sentence."
Akihiko actually sinks to the lameness of the aforementioned Ikutsuki at one point when trying to follow the advice of self help book that advised him to improve his self confidence by "having a sense of humor", and upon realizing this he actually bitches himself out for being so lame.
Shinjiro tries to hide his Real Men Wear Pink tendencies, but all he achieves is Epic Fail thanks to one third Aigis' being able to speak dog, very bad improvising skills, and the world's worst timing.
The lyrics to "Gekkoukan Boogie", the school song. "Everybody was Haiku writing...those kids were fast as lightning"
In the PSP remake, equip Shinjiro in a Tuxedo, add him in your team, talk to him and he'll go all Tsundere about it.
Shinjiro: Are you into this sort of thing?!? That's fine, but... Can't you see how out of character this is for me?
Equipping the female PC in the more provocative outfits such as the swimsuit or Battle Panties and then talking to Shinjiro is also good for comedy.
When Aigis finds you if you're playing as the female protagonist. Akihiko and Junpei arrive to see the girl they were trying to win over hugging you for dear life, and Akihiko says, "Oh, so that's her preference. No wonder we got the cold shoulder."
Interestingly enough, if Akihiko and Ken are lovers of the Female Protagonist in Portable they will be very flustered around her. In the English version, Ken's might even count as Getting Crap Past the Radar, considering how all the other Shotacon references got rewritten.
Whenever you fight Jin, his Idle Animation is mainly him doing a little dance almost in rhythm with the battle music.
Theo's dates are full of these. When you take him around Gekkoukan High School, he sits at a desk and asks you to play as teacher. You ask him a question and he doesn't get it.
He is what you've heard referred to as a "problem student"...
The Film Festival can provide several, based on who you took with you to the last week of it.
Aigis' thoughts after finishing the Ninja movie marathon.
Aigis: Ninja is the highest status man can achieve. But I wonder why ninjas ceased to exist? Was it an ice age? Or the proliferation of the internet? This is an enigma I cannot resolve.
She will then proceed to refer to the main character as [Name]-ninja.
You can take Koromaru to the movies. You get Courage points for trying, but you get kicked out anyway, and Koromaru pouts until you promise to buy him the DVD.
If you choose kendo as your sports club, Minato gets to try his hand at one of the matches at the meet during summer break. That said, he just whacks away like a lumberjack while his opponent is just crouched, taking all of it.
The Drama CD has lots of funny moments in it, but one in particular is when Minato goes to visit Elizabeth in the Velvet Room, and after a short conversation, Elizabeth gives Minato about 3,300,000 yen (keep in mind, that's about $30,000+ in US dollars)...in arcade tokens.
Fuuka: MC-kun, what do you think Christmas is about?
The fact that Koromaru can call for an All-Out Attack... but the dialogue itself merely reads 'Woof, woof!' (You can figure out what's going on thanks to the interface.) What your party members say to him in battle is even more amusing: