Timon and Pumbaa's reaction when told the new cub is a girl—they screech and faint. The fact that it caps off the title sequence is icing on the cake.
Timon: It's gonna be like old times! You, me, and the little guy! Rafiki: Hehe. It is a girl. Timon: Right, a gir- Timon & Pumpa: GIRL?! Oi... [faints] [Title Card and dramatic note]
After Kiara goes off to play, Nala starts to playfully tease Simba that Kiara is just like him when he was young. Simba doesn't deny this and pointed out the trouble they get themselves into by using the word "we". Nala playfully pins Simba and tells him that he means the trouble he put them in. Knowing that Nala is right, Simba chuckles at these words.
Timon and Pumbaa startle Kiara with a Reactive Continuous Scream, causing her to lose her balance and fall off the rock and into a pond.
Pumbaa: Oh, don't worry, Kiara! Uncle Pumbaa's comin'! [leaps into the pond after her] Timon: Oh, no! Uh, uh, let's see. [pretends to speak to Simba] Gee, Simba, the good news is we found your daughter. The bad news is we dropped a warthog on her. Is there a problem with that? Pumbaa:[looking around unaware of the bubbles coming out of the water around him] Kiara? Kiara? Timon: PUMBAA! Let me define... BABYSITTING! [Pumbaa moves away, revealing a spluttering Kiara. She coughs the water out of her lungs, as she glares at him] Pumbaa: Sorry.
When Kiara leaps onto the crocodile's snout clamping its jaws shut just before it could eat Kovu, you can briefly see that it has a look in its eyes that says "Really?".
During Zira's introduction:
Simba:Zira. Zira: Simba. [Simba's pride surrounds Zira, including Timon and Pumbaa.] Zira: Nala. Nala: Zira. Timon: Timon, Pumbaa. Great! Now that we all know each other,GET OUTTA OUR PRIDE LANDS!! Zira:Your Pride Lands?! [Roars at him] Timon:[screams, immediately hides behind Pumbaa].
When Simba prepares to scold Kiara for deliberately disobeying him, Nala pauses and gives him a knowing smile — clearly remembering the time Mufasa scolded him for the hyena incident in the first movie, and rubbing in her earlier comment that Kiara is just as mischievous, disobedient, and headstrong as he was when he was a cub.
Nuka is always good for a laugh.
When he and Vitani are setting the grass fire to trap Kiara (part of Zira's plan):
Nuka: Roasty toasty princess, roasty toasty princess... Hey, is it hot in here, or is that just me?[only now does he realize he has encased himself in a ring of flames and his tail is on fire] FIRE! YOWWW!
Prior to that, when in the geyser fields, he gets a face-full of geothermal gas.
Even in the Villain Song "My Lullaby" he's funny. "Kovu, what a guy," spoken unenthusiastically and completely deadpan while waving a pitifully small flag (think Genie cheering for Jafar).
When Zira says some of the lyrics, he proceeds to act them out, with him feigning death when she says Simba will die, and holding up Vitani by the tail when Kiara is squealing in her grasp, only to get rapidly kicked in the head by her.
Of course, him feigning death can be a lot less funny to watch knowing he dies in a gut-wrenching way later on the film.
His line "So you found yourself somebody, to chase Simba up a tree!" just makes you think "Bless you, you're trying so hard to be evil for your mother, but you don't quite get it yet."
When Rafiki is worried about Kovu, Mufasa (in the form of the wind) implies to him that the solution is to hook Kovu and Kiara up. Rafiki thinks the idea is ridiculous and mocks Mufasa for it—until silenced by the wind. Even when dead, Mufasa has a great sense of humor (and gets his way).
Rafiki: What? Kovu... Kiara... together? This is the plan? ARE YOU CRAZY?! This will never work! Oh, Mufasa, you been up there too long. Your head is in the clouds![wind blows hard at Rafiki] Okay, okay, okay! Alright! OKAY! I don't think this is gonna work, but I trust you. I just hope you know what you are doing!
Technically, as Mufasa is literally in the clouds, Rafiki isn't wrong with his "head in the clouds" comment.
Simba's enormous sigh when Kiara has her first hunt. It effectively is the moment where he goes "Oh, why did this have to happen?", and he really wants to keep her safe.
Similarly, his incredible reluctance to actually promise to let her do her hunt on her own. He predictably breaks it two seconds after she is out of sight.
During Kiara's hunting lessons, Kovu rolls his eyes and sighs as he can hear Kiara sneaking up behind him, counting down from three as he casually ducks from her attempting to pounce on him.
Kiara: You could hear me. Oh Kovu: Only a lot.
Timon demands a flock of spotted thick-knees to stop eating all the worms, only for one of the birds to bite him on the nose. Meanwhile, Pumbaa unsuccessfully tries to scare the spotted thick-knees away, and ends up having a whole flock perch on his back.
While Kiara and Kovu are helping Timon and Pumbaa scare away the birds eating all the best bugs. Then the group chases after the birds for fun, and promptly run into the birds’ friends... an entire herd of rhinos.
This then leads into Kiara, Kovu, Timon and Pumbaa running away. Kiara runs around a corner, screaming in terror, followed by Kovu screaming in joy and Pumbaa flies around the corner with Timon on him, shouting, “Hey, rhino!”
This leads to the scene in the cave, where Kiara and Kovu get an Accidental Kiss when Timon and Pumbaa try to get out. Both of them immediately get very flustered over the moment. However, it is also made very clear the two secretly enjoyed it.
The kiss itself is funny in that Kovu's eyes widen in shock when he sees what is happening, while Kiara's eyes are completely shut as if expecting this would happen, only for them to open and Kiara realizes just what happened. She can only mutter out an "Um" and that is it before she apologizes, with both of them nervously chuckling to each other over it.
When Kovu meets Rafiki, by way of the mandrill jumping up out of the grass before rapidly disappearing, he asks Kiara who it was in a panic. The little gasp of surprise Kiara gives before she calls him "Friend of the family" indicates that Kiara did not want Kovu to meet Rafiki in that manner.
During the final battle, Timon and Pumbaa find themselves being chased by four Outsiders. When they get cornered, Timon cocks Pumbaa's tail like a shotgun and points it at the lionesses. The kicker? It actually works!
Timon: Don't anybody move! This thing's loaded. I'll let ya have it! [the lionesses run away screaming. Timon twirls Pumbaa's tail, cackling] Talk about your winds of war.
The fact that Timon's first thought is to do that implies it has worked before!
This exchange before Kovu gets exiled:
Timon: Why I oughta...let me at 'im! Let me at 'im! [to Pumbaa] Here, hold me back. Pumbaa: Okay. [holds his tail] Timon: Let me at 'im! Let me at 'im! Pumbaa: Okay! [lets go, making Timon lurch forward] Timon: I think you're missing the basic point here. Pumbaa: Oh.
You gotta admit, this exchange during Kovu and Kiara's first meeting is worth a thousand laughs:
Kiara: My father says to never turn your back on an Outsider. Kovu: You always do what daddy says? Kiara: No! Kovu: Bet you do! Bet you're daddy's little girl!
It's meant to be sad, but during "Love Will Find A Way", a bush rustles and Kiara thinks it's Kovu, only to be disappointed that it is only a frog. Ordinarily, this would be a sad Bait-and-Switch, but the bush is so small that the idea that Kiara could genuinely think that Kovu could be completely hidden in the bush is actually unwittingly hilarious.
Kovu's major Parental Bonus when he and Kiara are reunited:
Kovu: Let's get out of here. We'll run away together... [wiggles his rear end and speaks in a suggestive tone] ...and start a pride all our own!
Timon just seems to make every dramatic situation a little lighter.
Zira: It's over, Simba. I've dreamed of nothing else for years. Timon: Boy, does she need a hobby.
And during the ending, Timon and Pumbaa cry Tears of Joy. All over a less-than-comfortable Zazu.
While Zira is a generally threatening villain, there are times where if you pause at the right moment (like when she is thinking about Kovu's "idea") she will have a very funny facial expression, like in the scene mentioned, where if you pause at the right moment, she will be cross-eyed and her mouth will have an :O look to it.
More dark (and possibly unintentional) humor, but the reactions from the Outsiders when Zira casually threatens her own daughter with murder can only be described as a collective disgusted scoff.
One lioness even mumbles "What a bitch!"
Another possibly unintentional humorous moment from Zira occurs in otherwise tragic scene, shortly after Nuka's death. When Kovu is stuttering, unsure what to say in response to Zira's accusations (and scarring his eye), for a brief moment you can see her making very bored and slightly annoyed expression that's just screaming "boy... use your words, would ya?".
The deep-voiced hippo in "One of Us." You can't deny he's a pretty good singer, though.
The mere fact that Simba was a troublemaking, mischievous cub in his younger days and ended up becoming a major Papa Wolf when he himself has a kid.
"HEY, YOU! HOW DARE YOU SAVE THE KING'S DAUGHTER?!" - Rafiki may be acting a little weird and crazy, but when you realise that he's successfully pulling off Mufasa's plan and no-one suspects anything because he's normally that weird and crazy, it becomes hilarious!
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