Ichiya's overdramatization about how he's not S-class and the Trimens joining in on it.
In-universe, Lelouch is trying not to laugh in hindsight that Wendy got on the wrong train when he and his guild broke for lunch.
Because of slight changes to his character due to PPRS, Jellal doesn't know what a prison bitch is. Cobra tells him he'll watch out for him and not to drop the soap.
Right before that, you have Midnight making fun of Cobra for having a soft spot for Kinana
Chapter 61 has Lelouch almost getting laid by Edolas Guinevere and freaking out from her getting touchy-feely. His reactions to pretty much everyone from Edolas Knightmare Frame are gold. Hell, Wendy's A-Cup Angst to herself provides a good laugh.
Chapter 64 has Erza rapping. It Makes Sense in Context, but doesn't make it any less weird. She also sings Rick Astley's Never Gonna Give You Up and dances the Hamster Dance, but that's just Erza being, well Erza.
Sindel's reaction to Mirajane's Takeover: Imp Soul is pretty humorous.
Later at the end of the chapter you have Airy talking about the idea of getting Fairy Tail's crest tattooed on her cute widdle butt and Mirajane apparently told her to have "more self-worth" or something like that. So, Airy puts it on her cheek.
Natsu and the gang's attempts to defeat Fenrir suddenly becomes reminiscent of Monty Python'sKiller Rabbit. In keeping in line with the reference, when Fenrir proves too much for the group, Gildarts beats it up in record time, leaving the group absolutely stunned.
Chapter 95 probably puts most of the examples already listed to shame. During the chapter, you have resident bisexual Freed find a trail of clothes that leads to a bush. Given last chapter, the reader might already figure where this is going—and even if they don't any Genre Savvy person worth their salt knows where this is going—and then Freed finds Airy and Loke having sex. Airy promptly covers herself and screams, clearly embarrassed by Freed's intrusion. Loke tells Freed to get lost, only for Mirajane to show up. Loke tries to avoid the inevitable destruction of his ability to have children by inviting Mirajane to joinin. This being Mirajane she actually seems like she might join in as she begins taking off her shirt, only to quickly switch to her Satan Soul form and begins attacking everyone, Freed included, as he tries to follow Loke and Airy to get them to put their clothes on. More hilarious is Loke lampshading Mirajane's sudden switch to joining in to attacking and Mirajane says she is joining, prompting Loke to respond that he's pretty sure she's not on the same page as him. The scene ends on both a serious and humorous note with Airy deciding to stop running and turns to fight Mirajane...except she's still stark naked. Freed lampshades this.
In chapter 110, Kagura returns to Mermaid Heel from a mission in a sequence that plays out hilariously similar to Erza's very first appearance.
Lelouch gets hamminess lessons from God Serena. To say nothing of Serena's congratulatory speech to Kallen for her christening as a member of the Ten Wizard Saints.
During chapter 117, Miala is having an internal monologue about how she and Nippy are partners only for Nippy to kill the mood and sneeze hot plasma in poor Meredy's face. Miala promptly tells Nippy to sit and he climbs off her back and whines like a little puppy.
Chapter 131 has Jellal and Ultear performing the fusion dance to become Ullal. However, since their consciousnesses don't merge and Ullal's body is female, the first thing Jellal takes an interest in is the new set of equipment upstairs. Ultear than takes command of the arms and slaps Jellal and calls him an asshole, telling him to focus on the task at hand beating Sting, Minerva and Rogue in order to win the Grand Magic Games. What makes it hilarious is picturing someone groping and then slapping themself since that's how it would appear to those watching.
The Yawgmoth Island arc has its moments when it's not being grim and serious. Special mention goes to Gino for sticking out like a sore thumb as comic relief, but Lyon and Sherry have some fine moments of Deadpan Snarker. And then there's Lloyd.
Chapter 137 might have one of the funniest gags in the whole fic. So, Kallen is going to Blue Pegasus to recruit members of them for a bodyguard mission. It Makes Sense in Context. Upon saying that the princess is in danger, Blue Pegasus' male populace start scrambling over each other to go on the mission. Master Bob phases through the crowd and politely tells Kallen to wait outside. Then, while Kallen calmly files her nails, Bob yells at his guild and presumably beats the tarout of them, but when Kallen comes back in the guild hall, everyone is how she first found them, except on their best behavior. Kallen even notes that she probably doesn't want to know how things got this serene.
When an issue of Sorcerer Weekly reveals Fairy Tail's return, there's already the first scene of the chapter involving it where Kagura does a Spit Take, but then we have a later scene with Sting. Lector brings him the magazine and shows him an article. This leads to a hilarious bait and switch where it seems Sting is reacting to Natsu coming back, only to find out that Lector was on the wrong page and Sting was reading an advertisement for sneakers.
Lyon and Sherry walk in onRakshata and Lloyd, with both characters quickly deciding to go grab the Brain Bleach. In Rakshata and Lloyd's defense, they did bother to lock the door. Sherry opened it forcefully with magic—adding another layer of hilarity to the scene—and only interrupted them because they were being loud. What then sells the scene is that even after the door is closed and Lyon and Sherry leave, Rakshata and Lloydkeep going.
There's also the Brick Joke spread out between 114 chapters. In chapter 48, the author tosses a brick into orbit. In chapter 162, it hits him on the head. Why? In both chapters, Lelouch and Erza go to a restaurant—albeit a different one—but they get thrown out for the exact same reason helping the exact same waitress.
Airy Kitsune just in general. If you don't find her to be profoundly annoying, she's a laugh riot.
Lector shows he's Not So Different from Happy as he uses the latter's trademark "You like her" with regards to Sting's relationship with Yukino.
During the dragon attack of the Envoy of the Future arc, Gino, Danielle and Tamara are teamed up. Gino, never one to take anything seriously asks if he can grope Tamara because since Anya is flat as cardboard, he'll never know what boobs actually feel like. Tamara, understandably, tells him to fuck off and then she and Danielle get into a whole argument. What really sells it is that they're still under the attack of a golden dragon and the two women become oblivious to it, focusing more on fighting each other and Gino doesn't even try and break them up. He just casually teleports the three of them around the dragon attacking them.
Also part of the dragon attack, After Future Nippy gets his past self under control, he tells Miala that he's sorry about the rug. Miala frantically hopes he doesn't meant the Casmire, but present Nippy's whining indicates otherwise. Miala's reaction sells it.
Miala: Nippy, sit!
CC provides us one of the funniest gags in the entire fanfic as part of the last chapter to go out before he hiatus. With the introduction of the new character Leaf, the bunny-eared Fish Out of Temporal Water hits on Suzaku, much to his mom's approval. Selina decides to set the two of them up. CC intervenes. How? Well, because Natsu is convinced that his future wife's name is Luh, she manages to get Suzaku away from Leaf and instead almost gets her laid with Natsu. This in turn causes Alice to demand what Leaf did to her baby brother, and subsequently gets EVERY SINGLE GUILD IN THE BALLROOM into one huge fight. Erza drags Lelouch into it, claiming they're going to "avenge the desserts" and Makarov apologizes to the king for the chaos. And what does CC do in all of this? Laugh her ASS off in a way Lelouch has never seen before.
In that same chapter, there's also Serena performing Cha-La-Head-Cha-La in English no less and Ichiya weeping Manly Tears at the performance.
Chapter 200 provides a good laugh in the form of dark mage Vanilla S. Chocolate. Her guild master, Ember, states that Vanilla's magic is useful for escort services. Cue Vanilla transforming into the primary example of a call girl, complete with Sex O Phone and Wolf Whistle provided by her magic accessory the Thought Paddle. Ember quickly corrects Vanilla's misinterpretation.
Whatever Erza did to Sindel to "educate her in romance" likely involved Erza's eroge collection, and "hands on instruction" and it's left mental scars on poor Sindel.