Some tales describe passersby stumbling across the remains, wondering how they got burned.
The description of the Zombie Cop describes how it enacts deadly force on any human being now that it's undead, as opposed to only when the situation called for it while it was alive. It adds that "threats of increased paperwork, pay cuts, or disciplinary action are all useless, as they are no longer government employees."
Believe it or not, the game over sequence is actually pretty humorous. The afterlife turns out to have quite the queue, and Charon basically tells you, in the most deadpan voice imaginable, to take a number and wait to be called.
In fact, there's so many numbers that Charon actually sells continues just so he isn't so overworked.
Mundane activities such as "To the Roof" being put under Quests.
(Your) Burroughs excited to tell the other Burroughs that you're becoming the best Samurai from your generation.
Walter teasing Jonathan that he goes to the bakery to get hooked up with girls.
Normally, Isabeau is always stoic, but when she discovers a certain manga set in France (strongly hinted to be Rose of Versailles), she briefly becomes some sort of excited Otaku.
Later on, after the group manages to corner the Black Samurai, she decides to mess with Isabeau by spoiling what happens at the very end of the manga. Isabeau's reaction is hilarious.
Nozomi constantly complaining about all three times she gets swallowed by demons in her third Challenge Quest.
After the group's adventure in Tayama's facility, they are faced with Yasomagatsuhi, who intoxicates them with a sweet-smelling scent that causes them to, in simple terms, get drunk. Walter declares his icthyophobia in a very hilarious manner, Jonathan announces that he's a cat and starts making cat imitations and Isabeau complains about seeing demons everywhere and eventually leaves with the guys. Finally, you lose consciousness... and when you wake up, you are alluded by Jonathan that you took off your pants and did something with your nose. He is then interrupted by a flustered Isabeau before he could continue.
Sometimes when you try to convince male demons to come with you by saying that they'll meet girls, they accuse you of being a pimp and call for the police.
Unintentionally funny with the Hooligan, who logically shouldn't even care about the police.
When a demon that has the "Data" personality (speaks entirely in binary-like gibberish) initiates Demon Whisper, Flynn's response when he's finished is a confused, "...Yes?"
The defeat of Peallaidh leaves behind his head... which gets tossed around round-robin due to how damn horrible it smells. Isabeau is the first to pick it up, before handing it over to Jonathan. Jonathan quickly gives it to Walter, who makes a crack about Jonathan and Isabeau being squeamish and touts the head as a trophy... before getting hit by the smell and giving it to you. The game's message log even announces each character "obtaining" the head in turn, as if they were receiving a plot-critical item you would normally get.
Pluto completely malfunctioning when you defeat it, it usual Machine Monotone turning into something halfway between a crashing program and dubstep (with a bit of Youtube Poop too).
About halfway through the fight, Pluto condemns the heroes and commands them to repair its functions, which results in Walter snidely replying and Jonathan misunderstanding and replying sincerely.
And then the moment you arrive and show the guard the proof, he apologizes in the most deadpan possible manner and lets you pass without another word. Walter's reaction is priceless, especially so when you consider what the "proof" was (a matchbox).
The Samurai you have to rescue from Tayama's clutches. At first, there is a lot of tension and drama as everyone tries to rescue him, but after invading Tayama's Hills building, nobody seems to care about the Samurai even if he's clearly being tortured. After some events, rather than leaving the top floor of the building after everyone's left, the Samurai stays behind to find more mystic relics to take home.
Akira the demon calls Jonathan and Walter with names. He first calls Jonathan a "Goody-Two-Shoes" which he doesn't understand, but Walter is seen smiling in the background...and then Walter gets called "bad boy," making Jonathan smile instead.
Hugo turns out to be a Henpecked Husband. Hearing him vent about his wife while attempting to remain civil (as well as TRYING to avoid giving away the fact he's the "acquaintance" he's talking about) is quite hilarious.
Recruiting demons in general, natch. One such example is trying to recruit a demon with a "beast" personality, where they ask the player to dig into the ground. The three possible responses given to the player?
There's another example of this, wherein the demon tells you that you have no choice but to bow down to him. As such, you get three choices all telling you to bow down.
Some demons can propose you a rather loaded question: which are stronger, humans or demons?
Other demons command you to die. If you obey ("X tried to die!") then either they'll become so disgusted with your disregard for your own life they'll leave, or they'll be so shocked at it that they'll immediately join you to keep you from doing it again.
The terminal guardian is a pretty hilarious guy. He appears differently with each appearance (once as a woman), and after being defeated the first time, freaks out each time after when he realizes that it's you once again to take his terminal. Later on, he becomes much more affable though still overconfident.
At the 9th terminal, he will summon Mara to battle you, and delivers this line (with appropriate Lampshade Hanging):
Terminal Man: "Even you won't be able to beat off this magnificent schlong."
Those chatting skills that lets you get macca, healing, or reducing press turns from demons? You can use them on bosses. Even on the The Whites!
The VR missions have some fun gems, such as Hairy Jack becoming a honorary Jack, or Demonee-Ho being your drill instructor.
Demonee-Ho: "Private Hee-ho! I will unscrew your head and hee-ho down your neck!"
After retrieving Osiris's body parts, he joins you on your quest. After his wife Isis leaves though, he makes mention of a certain part missing. Considering his mythology...
In the Law or Chaos paths, try resting in the barracks or having lunch at the Hunters' Association. Merkabah and Lucifer will still walk up to you to wake you up, or wish you luck while eating the "ersatz" concoctions, as if it they were still your old partners.
While the visits to Blasted and Infernal Tokyo are in general pretty dreary, and naturally so because the White are trying to drive Flynn across the Despair Event Horizon, there's one moment in the latter level that's pretty amusing, involving going into a lab run by demons and getting sterilized... by a Kanbari.
In the Cathedral of Shadows, if you accidentally try to fuse a demon without selecting any skills for it to inherit, Mido makes a hilariously flippant, miffed-sounding "MMM!" noise.