CobraBubbles seems a lot less funny when he comes to take Lilo away. Even worse is Nani's slow, horrible realization that she can't stop him, and Lilo's total incomprehension of what's going on. That and the fact that Bubbles truly seems sorry for what he has to do and does genuinely care about Lilo's well-being.
Later on, when Lilo is kidnapped by Gantu, and Jumba and Pleakley have refused to help, Nani crumples heart-breakingly, truly believing she'll never see her baby sister again. And just before that, she happened upon Jumba and Pleakley arresting Stitch, and asks them about her little sister. When they start playing dumb, Nani gets furious at them, and her voiced frustration is rather heartbreaking to listen to.
Nani: Lilo! She's a little girl this big, she has black hair and brown eyes and she hangs around with that THING!
As well as:
Stitch: I'm lost.
"Lost" translates into Hawaiian as "Lilo". In a way, It's almost like he's calling out for her.
It gets worse when you consider the implication-that he's emulating the story of the ugly duckling, in the hope his family will come and find him, like in the story...
Also, the conversation that ensues when Jumba finds him the next morning.
And this quote from Lilo as Stitch makes the decision to leave (roughly paraphrased):
Lilo: Our family is little now and we don't have many toys... but you can be a part of it. You can be our baby and we'll raise you to be good. But if you want to leave... you can. I'll remember you though. I remember everyone who leaves.
It's not even just what she says, but the matter-of-fact way she says it. This girl is 5 years old and has dealt with so much loss that it's become almost a normal occurrence to her.
When Nani and Lilo sit in a hammock in the backyard; Nani is looking for a way to possibly tell Lilo goodbye without alarming her or making it seem like they'll be forever separated, but Nani can't articulate the message through all her pain and sadness. So she sings the most beautiful, depressing rendition of Aloha Oe and...
In the beginning when Nani and Lilo are making up after their fight, when Lilo says "I like you better as a sister than a mom," then starts to cry and asks, "And you like me better as a sister than a rabbit, right?" It was so perfect because it's SO what a little kid would say — not very articulate, not even making much sense, just so terrified that her sister really doesn't want her.
Any of the strong Nani and Lilo scenes (especially the backyard scene) are tear jerkers for someone with an older or younger sister
Any time Ohana is mentioned.
Lilo: You came back... Stitch: Nobody gets left behind.
Tears were shed during the "Aloha 'Oe" part on the night when Nani and Lilo were talking about family for what could have been the last time as Lilo was to be taken into child custody soon.
"I remember everyone who leaves."
"This is my family. I found it all on my own. It is little, and broken. But still good. Yes. Still good."
Pleakley is moved by this scene so much that he glumly asks if they couldn't just let Stitch stay. It's the sad tone in his voice that makes the moment.
This deleted scene, featuring the death of Pudge the fish. Thank Disney, that the suits actually veto'd the scene.
Lilo: What's wrong with you?!? Stitch: [looks guilty and confused] Lilo: Pudge was part of our family! You don't let your family die! You don't EVER!!!
Lilo wishing on what she believes to be a falling star for a friend. The look on Nani's face as she overhears the wish says it all.
When Lilo explains what happened to her parents to Stitch: "It was rainy, and they went for a drive."
When Lilo's teacher asks her why it is so important that she bring Pudge the fish a sandwich, she says that he "controls the weather". Given that her parents died in a car crash on a stormy night, she is clearly trying to "appease" what she believes is the spirit that killed her parents so that no more of her family will die. The looks on the adults' faces when they realize that make this even more heartbreaking.
Is that what it was? It looked like they thought she was a little odd.
It could be both. They know why, and to the adult mind they know it won't help, and is probably actually harming her. But they don't say anything because they don't know how.
A scary thought: What if Lilo believing Pudge was in control of the weather was a more recent development? What if Pudge was originally nothing more than a defacto pet she'd been feeding sandwiches until then? What if the day her parents died were the one day she forgot or was too busy to feed Pudge? This could mean that she sees her parent's death as her own fault for forgetting to feed Pudge.
Then we come to understand why she reacted quite violently when Mertle called her crazy. She took it pretty personally.
After Cobra Bubbles tells Nani he REALLY has no other choice but to take Lilo away for her own good.
David: You know, I really believe they had a chance [to remain together]... but then you came along
This was followed by Stitch's slow realization of what he just did.... Ugh... It's so gut-wrenching.
Stitch's confession of being an alien is one for both him and Lilo. For Lilo, she was very forgiving of Stitch despite his shenanigans, but after nearly drowning and then having her house destroyed, and being taken away from her sister, she finally loses it and tells Stitch that he has ruined everything. After his confession, she's surprised, but the suddenly shoves him away from her and tells him to go away, not with shock, but with bitterness. For Stitch, he had honestly grew fond of Lilo and has done everything he could to protect her, but in the end, his remorseful expression after he changes back to his alien form, really hits you hard with how he knows that he has let down the girl who had adopted him and cared for him, and her shoving him and telling him to leave really hurts as well knowing that he has been abandoned by the only one who has ever genuinely loved him.
Earlier on, after Stitch has torn up the room as he does, Jumba muses that now there's nothing left for him to destroy. Since he never built Stitch for anything else, there was nothing left for him.
"What must it be like, to have nothing? Not even memories to visit, in the middle of the night..."
Lilo seeing Myrtle and her posse in town and gleefully exclaiming "Hey! It's my friends!", even when it's been explicitly shown that they hate her, and consider her their enemy. Owtch.
Nani at wits end after Gantu kidnaps Lilo screaming and sounding completely helpless when she finds Jumba.
"LILO! SHE'S A LITTLE GIRL, THIS BIG, HAIR LIKE THIS, AND WAS HANGING AROUND WITH THAT THING!!"
Lilo & Stitch 2: Stitch Has A Glitch
The climax. After malfunctioning and accidentally attacking Lilo, Stitch decides that it is too dangerous for him to live on Earth anymore and tries to escape to an uninhabited planet using Jumba's ship. Lilo ends up chasing after him with a hovercraft, and witnesses him crash into a mountain. Knowing the only way to save Stitch's life is to put him in Jumba's Fusion Chamber to recharge him, she activates the machine with Stitch inside, but he doesn't awaken. Lilo believes him to be dead and cradles his motionless body in her arms until Stitch suddenly grabs her arm, revealing that he did in fact survive.
Actually Stitch did die and Lilo's love brought him back. Makes it more sad, doesn't it?
"Stitch sorry." He says it so many times throughout the movie, but doing it right before he died... And before he says it one last time, as Lilo peers into the chamber, both hands on the glass, he reaches up and places his paw on the glass where Lilo's hand is. Possible Shout-Out to Spock's death, anyone?
The fact that it was so drawn out. They did the scene very well.
Jumba's entire story in the film is fairly sad: he finds out early on that Stitch is malfunctioning and dying, and spends the entire movie unsure if he can truly do anything to save him but tries his hardest to do so anyway. Elsewhere in the series, Jumba rarely makes it as evident that he looks at Stitch as his own child, and his pain as his attempts to save him fail is heartbreaking - when it looks like the only machine that could fix things has exploded, he just shuts down entirely. Luckily Pleakley is there to re-encourage him, but still...
"Jumba has failed family..."
During the film, Nani and Lilo have another small fight - which ends in a heartwarming way, but has this very tearjerking exchange, with Lilo being generally frustrated and Nani being increasingly agitated trying to help.
Lilo: (shouting) "You're not help! I wish Mom were here!"
Nani: "I'm doing the best I can!"
Lilo: (nastily) "Well, it's not good enough!"
Nani: (voice breaking slightly) "Don't you think I know that?"
The flashback scenes of the original movies, but then comes the real tearjerker scene. After waiting in vain for Lilo to appear at the beach like they had promised, Stitch thinks Lilo abandoned him so he grabs the tiki necklace from the third movie, hangs it on a tree and leaves the island on Jumba's ship. The sobbing hasn't even begun, though, because there's nothing more heartbreaking than seeing Lilo running towards the beach, finding nothing but the necklace and then hold it against her chest before screaming his name and falling to her knees, sobbing histerically. That single scene is enough to make you sob for the rest of the day.