Lechter's long string of Refuge in Audacity moments in Chapter 3. In particular, his skipping out on a fancy party to go fishing... in his host's ornamental pond. He then feeds his host's fish to his host's cat, who he's decided to rename. Later when all hell has broken loose, he uses that same cat and Exact Words to hide your party from some rather angry Mafia thugs, while making it sound like he was going to turn you over to them.
The entire scene that starts when bringing KeA to St. Ursula, with Cecile immediately assuming she's Lloyd's daughter and getting upset at his 'betrayal'. It takes Lloyd a few minutes to get through to her that there's no possible way he could have a daughter. Whoever is your partner at the time will lampshade Cecile's weakness where Lloyd is concerned.
The entire quest involving Anton and Fran in Zero is one of these, in large part because Noel is in your party at the time. During the date with Fran, at the end as Anton gives her the present he asks if she has a boyfriend. She says she doesn't but there's someone that she loves. The music stops, then the game over music plays, in a moment of Crowning Music of Funny. After he leaves, her overprotective older sister Noel runs up to her and demands to know who this person is and if it's Lloyd or Randy. As it turns out the person she was talking about was Noel.
The drama cd version takes this Up to Eleven with Noel proposing increasingly unlikely candidates for Fran's special someone. She finally stops after she reaches Zeit. Then the scene ends with Fran declaring that if she can't marry Noel, she'll never get married until Noel does, met with mass presumed facepalming from everyone else present.
During Tio's IBC event, Lloyd muses on how it took Guy forever to notice what Cecile felt about him and that sometimes he felt like kicking his brother to make him realize what was right in front of him. Upon hearing this, Tio immediately kicks Lloyd.
Ao no Kiseki
During an investigation, the SSS has to ask a shopkeeper for information about strangers in Crossbell. Afterwards, the justly worried mother asks her daughter if she's seen anybody strange around town. In response, she gets told that she was just talking to some strange people. She then mentions the other strange people she's seen around recently: Ries and Lechter.
The fortune-telling scenes in Ao can be heartwarming, tearjerking or foreshadowing but some of them are just plain hilarious. Tio for example wants to know how compatable she is with Michey. As a fan it's reallyimportant.
Heck, most of Michelam is funny, whether it's Lloyd trying to apply sun oil or Tio giving a serious lecture on the awesomeness of Michey or Randy planning out his flirting schedule in advance or KeA innocently asking if she and Lloyd could get married when she turns sixteen.
One that's purely visual: After exhausting all your Tickets, you'll leave the theme park in a cutscene. Tio turns back to wave at Michey. And stops to do it again. And again. Did we mention she's a huge fan?
Upon completing KeA's room ornament sidequest, you're treated to a scene featuring a callback to Zwei II in which KeA wears her penguin costume. As the other SSS members file into the room, the girls all rush over to KeA and begin glomping her, bowling Lloyd over each time. The scene ends with narration informing the player that the SSS set up rules about KeA and that costume after the fact.
One of the hidden quests involves Sully training before Arc en Ciel's big renewal. Ilya tells her to take a break to eat something and begins talking to Lloyd and the others as Sully dashes offstage. She dashes back on stage about twenty seconds later, declaring that she's finished eating.
The entire reunion with Tio in the Final Chapter of Ao, starting with her forgetting that her armor makes tight hugs uncomfortable for the other person, then her delayed realization that for the first time, everyone can hear what Zeit is saying.
When Randy confronts Gareth, the latter asks what Randy thinks he's doing confronting him when he has a Blade Rifle and Randy doesn't. Cue Randy pulling out his Berserga (which is considerably bigger than Gareth's weapon) and pointing out that he has one, he just didn't need to use it. Cue Oh Crap reaction.
Randy flirting with Duvalie as the latter is challenging the party to a fight, throwing her completely off script.