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.
Many people don't distinguish between "Alice in Wonderland" and "Through the Looking Glass" (or simply don't know), and the film's mingling of the two exacerbates this.
Ear Worm: Pretty much every song, but especially those you hear at the Mad Tea Party.
"A very merry unbirthday to you!" "To me?" "To you!" "Oh me!"
"I'm late! I'm late!"
"Forward backward inward outward come and join the chase! Nothing could be dryer than a jolly Caucus Race!"
Memetic Mutation: People telling the Queen to shut her trap seems to be pretty popular.
Even Disney themselves did this: In the 2008 documentary Picture Perfect: The Making of Sleeping Beauty, a clip of the Queen of Hearts plays when discussing Verna Felton, who voiced the Queen of Hearts, Flora the Good Fairy, and many other Disney characters. She bellows, "Off with their heads!", before the documentary cuts to Fauna exclaiming, "Now dear, that isn't a very nice thing to say!" Whether the makers of the meme received inspiration from this currently seems unknown.
Moral Event Horizon: The Cheshire Cat needed only one line to proof that he has crossed it: "Well, she simply said you're a fat, pompous, bad-tempered old tyrant!".
Tear Jerker: "Very Good Advice", which is pretty much "Heroic Self-Deprecation: The Song". Also an in-universe example, as the song ends up having all the Ugly Cute birds in the Tulgey Wood start crying with sympathy while she sings.
Ugly Cute: The animals in the Tulgey Wood. Especially all the strange looking birds. Who's a cute widdle living birdcage?
The Glasses Birds especially. They're pretty much Adorkable personified (as birds).
The Cheshire Cat, although he's more "Creepy Cute". Alice's reaction when he first shows up implies that she thinks this too.
Vindicated by History: The film opened to a lukewarm box office and mostly hostile reviews in 1951. Walt himself voiced Creator Backlash against the film and famously declared that it had failed because "Alice lacked heart" (it's somewhat unclear whether by "Alice" he meant the film or the character). In the decades since, it has become better regarded by both critics and general audiences and is now thought as something of a minor classic.
Interpretations that the White Queen is evil are not uncommon. This is actually an interpretation somewhat supported by Anne Hathaway, who claims that she tries as hard as she can to not give in to her "inner darkness".
Alice at the end: Oh, this is fun... Did she leave her Wonderland because there's no place like home, or because she realized Underland was just as restricted as Victorian England because destiny says so, and home is a little more free.
Did she travel to China to become a woman of the modern, career-driven feminist archetype? Or is she going to ditch the company first chance she gets and return to Underland? Hey, before she sailed off she'd pretty much wrapped up her life in England, canceled the engagement, set her brother-in-law straight, said goodbye to her mother and sister, and most importantly, ensured her father's dream reached beyond the limits of his life.
When the Knave of Hearts is told he will be chained to The Red Queen for the rest of their lives, he immediately draws a weapon before being disarmed. Was he about to kill her... or himself? Or was he going to kill the White Queen (or both queens)? The latter interpretation would account for the Hatter's pissed-off look when he threw the scissors to disarm him.
How about Aunt Imogen's dreams of a prince who can't marry her? Perhaps she was left at the altar by a former betrothed (or engaged to someone who died), and she clung to her delusions rather than accept the painful truth.
The Jabberwocky seemed like a pretty cool guy. You probably could have made a deal with him to leave the field if you'd just given him the stupid sword, Alice. Given that the Jabberwock is the only one who stuck with the Red Queen by his own free will (all the others were just afraid of him) instead of just toasting the wench, it is probably safe to assume he is really her loyal pet, or a kind of construct at her service, or simply an immensely evil being amused by the sight of Underland suffering the tyranny of the Queen.
The Cheshire Cat and the Mad Hatter's Hat. He brought it on himself.
The White Queen can make furniture fall in love with her. Although that could be a reference to the fact that the role of most furniture is played by animals in the Red Queen's kingdom.
The Jabberwock and the Vorpal Blade sure seem to have a lot of history.
Crack Pairing: Alice/Mad Hatter gets in with a bit of UST. The pairing was originally intended to be canon, according to an early version of the script. Strong hints remain in the film's novelization and one of the visual guides, which states that "Although Alice and Tarrant (The Mad Hatter) do care for each other, they are not compatible because she is always either too tall or too small."
For some, Mad Hatter/White Queen is the preferred ship, and actually receives a bit of supporting evidence in the video game adaptation. Since neither one is precisely sane, it gives a new meaning to Crack Pairing.
Critical Dissonance: It received mixed/average if not negative reviews from critics, but broke $1 billion at the box office.
I Am Not Shazam: As everyone who's read it knows, Jabberwocky is a poem, and the creature that's slain in it is called the Jaberwock. But in this movie, the monster itself is called the Jabberwocky.
Narm: The futterwacken. Maybe if it was more like a Highland reel?
Nausea Fuel: Alice crossing the moat of heads; later, the White Queen's recipe for pishalver (shrinking potion) which includes "buttered fingers", horsefly urine, and spit.
One-Scene Wonder: Marton Csokas as Alice's patient, loving, slightly-odd father in the very first scene of the film.
Purity Sue: The White Queen when we first meet her. Everyone loves her, she won't hurt a living thing, and her lethal cooking turns into a save-the-day cure. According to the actress, her over-the-top "princess" mannerisms are the character overcompensating for fear of becoming evil. Note how much more naturally she behaves in the scene with the dog after her courtiers have left.
They Wasted a Perfectly Good Character: You get Christopher Lee - Christopher Lee - to voice the Jabberwocky...and you only give him two lines and then have Alice cut his tongue out? Why does he have an enmity with the Vorpal Sword? Why does he stick by the Red Queen's side? We'll never know because you sliced off his tongue!
Uncanny Valley: Aside from Alice, every single character, even the ones that are supposed to be neutral or the good guys, look unsettling as hell. To put in perspective, the Cheshire Cat with his perma-grin looks the least scary.
The Untwist: Alice turned out to be the right Alice after all.
What Do You Mean, It's for Kids?: People gripe about the basic plotline and lighthearted tone—only to be shocked when they see that it is, in fact, targeted towards children.
What Do You Mean, It's Not Political?: The movie is arguably a result of Burton running with the theory that Alice's Adventures in Wonderland was at least in part political commentary of the Wars of the Roses, with the Queen of Hearts being combined with the Red Queen of Through the Looking Glass (thus taking the possible symbol of "painting the roses red" — possibly an allegory for Lancaster aggression against the house of York, which was symbolized by white roses—and combining it with the imagery of Red (Lancaster) and White (York) Queens going to war). Evidence for this interpretation includes Johnny Depp's deliberate switches to a ridiculously over-the-top Scottish accent whenever he talks about rising up against the queen.
The Woobie: The March Hare, who comes pre-broken (and to get this out of the way, arguably, the Hatter in his less subversive moods).