After Keetongu refuses to change them back into Toa:
Matau: So we came all this way JUST TO FIND OUT WE DIDN'T HAVE TO COME ALL THIS WAY??!
One poor Visorak has been relegated to janitor duty but is slacking off... until Sidorak walks by and suddenly it's buffing the floor.
A personal little laugh this troper gets is back when Takua was in Metru-Nui there was a running joke that an entire squad of Vahki(Which was at the time Metru Nui's police force) was assigned just to keep watch on Takua.
That characters just flip small animals instead of coins to end quarrels. The Piraka also liked to flick each other. It would be such a surreal sight to witness these 7 foot thugs randomly flipping each other over, that it's plain funny.
This leads to an incident where Mutran and Chirox are having trouble settling a disagreement due to the nearest Rahi being a creature with two heads, one on each end, and no tail.
In The Mutran Chronicles, Mutran taking claim for the creation of the Lohrak, when Chirox already made it. Chirox is not amused.
The entirety of "The Mutran Chronicles" is a crowning moment of funny for those who like a little dark humor.
Lewa telling Kopaka and Onua the story of the three Matoran, the Rama swarm, and the basket of Bula berries. The story itself isn't all that funny- it's the fact that Kopaka is getting progressively more and more annoyed and shouting at Lewa because they're in the middle of a battle.
Onua: At least the Makuta seem to be keeping their distance. They must have heard Lewa tell a story before.
Kopaka: I'm still waiting for the part where the heroic Toa Lewa saves the day!
Lewa tries to tell a story. Kopaka interrupts with the 'short version'.
Lewa: Some storyteller you are...
For some reason, the Phantoka Makuta literally getting their eyes burned out by the intense light that burst from Matoro's Heroic Sacrifice was pretty funny. From their perspective, they just saw a random Toa fall from the roof of the cavern, and then suddenly they were blind. Mutran, on the other hand, casually notes in his last blog/diary/chronicles before the Toa arrive:
Mutran: Hmmmm... what’s that? I could have sworn there was a flash of light outside. It must have been pretty powerful for me to see it all the way in here. Well, I suppose if it was anything important, I will find out about it in time...
When Vezon, after having a Mask of Dimensional Gates fused to his face, ends up in an alternate timeline where Toa and Glatorian work together on Spherus Magna, he gets into this conversation with Tarduk:
Tarduk: So who are you, exactly?
Vezon: *loud enough for everyone to hear* My name is... ah... Toa Vezon. I'm the Toa of... of... Anarchy.
In Maze of Shadows, when Matau asks why doesn't the Karzahni plant get the vial of energized protodermis itself, the plant replies back that it wasn't created with mobility.
The Credits Gag at the end of Legends of Metru Nui, which includes fake positions written in Matoran script (for example, "Assistant to Mr. Makuta").
In one of the books about the Toa Metru, Onewa is attempting to find Ahkmou and get the location of the Great Disk of Stone from him. He finds him sitting on top of a very large structure, and while Onewa is running and busting his tail to get to Ahkmou before Nidhiki can, Ahkmou very casually yells down to him, "Hey, Onewa, what gets harder to catch the faster you run?" Onewa, who is very much not amused, immediately shouts back, "MY BREATH!"
Nidhiki was wonderfully snarky during his appearances. Notable examples include:
"You take all the fun out of constant violence, Lhikan."
"Hi, honey, I'm home!" (said to Tuyet after she becomes a monster and is about to kill Lhikan)
"A friendly place we have here. Heavily defended, home to several hundred killers, and unfailingly lethal to trespassers, but friendly."
"I see you have spirit, little Toa. I hate spirit."
Much of what Vezon has to say is hilarious. Then again, he was apparently inspired by Deadpool, so...
When Trinuma tells Vezon that the Order of Mata Nui needed someone who could die without being missed and had naturally thought of him, Vezon has to take a minute to think about it, and then decides that it's a compliment.
"Well, naturally! Lead on, and let me show you all how dying's done!"
When being told that he has to help Roodaka and several other villains who are being forced to find Miserix, Vezon's only reply is that, OK, they can take him home but they'd better not expect Vezon to clean up after him.
Turaga Vakama beating Lerahk over the head with his staff in Mask of Light to little effect was hilarious, especially since the obviously confused Lerahk was just standing there and letting him do it.
Hahli: You're insane!
Karzahni: I prefer the term "creative". Though I suppose there is not much difference between the two in the end, is there?
Mutran and Chirox's bickering has a certain comedic element to it. Mutran at one point muses that usually he disposes of failed experiments, but in the case of "this hissing, biting, and incredibly toxic creation", he'll make an exception and present it to Chirox as a gift.
He also once had a pet rock that he accidentally left behind on a certain island during a mission there. Though disappointed at losing his project, he shrugs it off and forgets about it. Fast forward a few thousand years, and the thing has somehow grown into a carnivorous mountain.
Antroz makes his own rhymes in the middle of battle with Pohatu.
All of the Brotherhood of Makuta were quite well-versed in the ways of the Deadpan Snarker.
Nuju would rather die than spend time with Matau.
Tahu would like to know Onua's thoughts on how to proceed into battle. More importantly, are there any explosions?
At some point in a story from 2005, the Shadowed One was asked if someone's hand should be cut off for insubordination. He replied that enough hands had been removed that year, referencing the amount of hand-chopping in the Star Wars movie that had been released a few months prior.