The game opens with Layton explaining the witch trials of the medieval ages and how there weren't really any witches. Enter the Damsel in Distress, and then the pigeon that transforms into a clawed one-eyed thing that blows up the office and kidnaps their client.
Luke: What was that?! Layton: (calmly and with utter confidence): That, my dear boy, was a witch.
And a little later:
Luke: Espella's been kidnapped! Layton: [Flatly] Yes, that was careless of us.
Wright greeting Layton: Not some normal conversation, but instead, WELCOME!, even with according, Objection-like speech bubble and a desk slam. And a cloud of flour, as he's working in the bakery.
When he's giving Layton some walnut bread, he slams the desk again (kicking up another flour cloud) and shouts TAKE THAT! at him, then points as the Objection theme plays. Maya tells him to cut it out, and he switches to embarrassed mode as the music dies.
Phoenix: I don't know why, but... I just get the urge to point and shout like that sometimes...
Luke and Layton's perplexed reactions to this.
The start of the first Witch Trial, where Phoenix is told to introduce himself... "My name is Phoenix Wright, ace baker!" What's better? The line is fully voiced.
The end of the first part of the first witch trial. The case seems all but won, and then... There's a "HOLD IT!" in a voice you've never head before. It turns out to belong to... some guy in the gallery. No really, his actual name is listed as "Some Guy". He loudly and hammily proclaims himself to be the "fifth witness" who will single handedly-save this trial, and calls the other witnesses into a huddle. The Judge, Prosecution and Defence are all equally baffled.
At the end of the first witch trial, Layton and Wright dramatically point together as Back-to-Back Badasses. For the second trial Layton is a golden statue, so it doesn't seem like this'll happen again... until the moment comes for the dramatic accusation, and Luke and Espella turn the statue in time with Phoenix's movements.
Inquisitor Barnham valiantly attempts to stop Phoenix from inquiring about the Alchemist's neighbour, who turns out to be Emeer. The reaction when Emeer takes the stand, from both Barnham and Nick, is absolutely hilarious.
Phoenix: (Oh dearie ME.)
Similarly when you disprove his testimony:
Phoenix: That gem was useless. Barnham: Pssh. Just like everything else this witness says.
Pretty much every instance of Phoenix and Barnham tag-team insulting this character is comedy gold.
Lettie Mailer's loudness:
Mailer: SIIIIIIIIIIIIIIIIIIIIIIIR! SFX: [microphone feedback tone] Phoenix: (I wish I had some earplugs with me...)
And then Maya notices something. In total, everyone at the reunion drank 17 cups of tea. So she thinks, maybe Layton has a rule about tea. Maybe he always has 17 cups of tea with every puzzle. Ace Attorney fans are doubled over in laughter about now. And then Phoenix quips that that particular Ace Attorney reference probably isn't appropriate, as the reference is about a big coffee drinker.
Phoenix has a new, cocky pose where he places his left hand on his hip and looks pleased with himself. It just oozes sass.
The cameo scene with Edgeworth at the end of the game. Also doubles as a moment of awesome.
It's dark humour...but it's still funny: When investigating The Legendary Fire, the team move to a vantage point to help them visualise how it must have appeared to one particular witness. Maya notes that to really put themselves in the witness' shoes, the whole town should be on fire. She then offers to go and get some matches.