These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Ass Pull: In "Angel" Lilo only finds out Angel is working for Hamsterviel because of a tag she saw around her neck on the video Pleakley took. Angel never wore the tag any other time.
The T-Rex at the end of "Retro". We never see how Retro made that. Though it could be assumed that he used his powers on a chicken or some other type of bird.
In "Snafu," Angel releases everyone from their pods by knocking her head against the glass. But wait, why didn't she just do that earlier?
Dude, Not Funny!: Nani's treatment of Stitch sometimes gets this, most notoriously in "Phantasmo".
Ensemble Darkhorse: Angel (#624), who recently got her own toy (only at Disney Parks, though) And of course, Reuben (#625).
Many of the other experiments as well, most noticeably: Sparky (#221; popular enough to be a mandatory Boss Battle in Kingdom Hearts: Birth By Sleep), Yin (#501), Yang (#502), 627, Bonnie (#149), Clyde (#150) and most peculiarly, Slushy (#523).
Fan-Preferred Couple: As of Feb 16 2011, there are no stories involving Lilo and Keoni Jameson (her crush in the series) on Fanfiction.net; there are quite a lot that pair her up with Stitch. Squick or Squee.
Ho Yay: Pleakley. True, it can be given in the beginning his "aptitude" with Earth customs is lacking, but early on... he openly tries girl's clothing. Also seems to crush on Jumba. Ironically, this seems to be a Disney subversion of Hide Your Lesbians.
The Very Special Episode where Pleakley's family try to make him get married - he's very reluctant until the 'bride' is Jumba in a dress, and in the end his family accept that Pleakley's happier without a wife. He also promised to wear men's clothes, which set off the lie detector experiment. Meaning he intends to keep wearing women's clothes and never has any intention of ever wearing man's clothes.
Actor Allusion, Actor Allusion, Actor Allusion! Pleakley is voiced by Kevin McDonald, of Kids in the Hall fame. The man is used to playing characters in dresses. Not only that, but his family members in said episode were voiced by old castmates Bruce McCulloch, Mark McKinney, and Scott Thompson, with Dave Foley playing the priest.
Jumba's Voice Actor, David Ogden Stiers, came out of the closet in early 2009.
"Jumba and I have found the secret of love!" Oh, Pleakley.
Hunka Hunka's peck, which causes the target to fall in love with the first person they meet, is decidedly gender-blind, leading to at least three instances in the episode where a male character falls in love with another.
Fibber's buzzing noise and Belle's scream, though that's kind of the point.
The "Ohana" speech. Proof that, with enough repetition, anything can be unbearably annoying.
Tear Jerker: In the Halloween special, we get Spooky who can shapeshift into people's worst fears. For Lilo, he turns into a Monster Clown. For Stitch, he turns into water. For Jumba, he turns into his ex-wife. For Pleakley he turns into his mother. What does he turn into for Nani?
The Scrappy: Keoni. He's a bland Audience Surrogate that adds nothing to the plot, and Lilo's crush on him tends to bring out the absolute worst in her. Even the writing staff hated him.
They Wasted a Perfectly Good Character: Victoria, the red headed girl Lilo befriends. It's obvious the writing team struggled with her then just gave up altogether. A pity, she had a cute design.
They Wasted a Perfectly Good Plot: In the episode where Lilo is hypnotised into acting like Mertle, they missed a perfect opportunity to have Mertle say Lilo was acting weird. Instead one of Mertle's friends points out that Lilo is acting like her and nothing more is said about it.
Also the episode "Dupe": Gantu finds four unactivated experiment pods and turns them into a Four Man Strike team against Lilo and Stitch. After their defeated in the climax of the episode, the experiments never show up again, save for the finale, "Snafu", where their Gantu's prisoners.
Viewer Gender Confusion: Quite as few people mistook Pleakley for a woman. Which is fairly easy to assume, since he only wears dresses, and disguises himself as a lady in public.
Yin gets a lot of this as well. An extremely feminine experiment, he/she is often labelled a female by viewers (not to mention several wikis), despite Lilo referring to him/her as a male repeatedly.
Villain Decay: Gantu turned from the imposing but somewhat Anti-Hero thirty-something foot tall military captain from the original movie into a much shorter bumbling idiot who even proclaims that he "likes to be evil". Subverted at the end of the series when it doesn't work out for him and gets his old job back.
What an Idiot: Houdini is an extremely timid, extremely gun shy experiment with the power to make things disappear. Where does Lilo reckon his "one true place" lies? As a star magician on TV, naturally.