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.
The Other Mother. Some say her only desire to eat children's lives; others say she's a Woobie who truly wants to love and be loved but just can't control her hunger.
Alternately, she might not see the difference between loving children and eating their lives. Just like how she doesn't see the difference between loving someone enough to know what's genuinely best for them, or giving them everything they want.
Big Lipped Alligator Moment: The audiobook version has a weird song sung in the middle of chapter 5. It's related to the plot of the story, but comes out of nowhere, is the only one, and is never touched upon again.
Knowing that the movie was originally planned as a musical with songs by They Might Be Giants, it's probably fair to say that a good number of these were averted. The song "Careful What You Pack" (which eventually wound up on Their 2007 album The Else) was originally written for this movie, and damn but it's catchy.
The official website has a section where you can add button eyes to pictures. Let your imagination runs free...
Coraline's hat has gained quite a following too.
Real-life example: A contest was held on the official site, where winners would receive custom-made Nike Dunks sneakers, which are made to look stitched together with patches, feature big, black buttons on the sides, and the soles are blue with white stars, much like the shirt the Other Mother makes for Coraline.
Paranoia Fuel: The doll. Think about it. A foreign object that transforms and moves around your house when you're not looking. And it turns out to be the Other Mother's spy. Which implies the other mother can see through buttons. Sleep tight.
Toy Ship: Coraline and Wybie. Most of the time, it seems this trope is the main reason why the latter was added to the film version of the story, even though Word of God states that it was because he didn't want Coraline to be lonely and talking to herself. It's still painfully obvious on Wybie's side, though.
And that the producer Bill Mechanic wanted Selick to put in lots and lots of kids. Adding Wybie helped Selick to satisfy that need as well.
Not to mention the Other Mother's skin in her final form.
Gaiman is something of a fan of this trope. Half of the persona for Islington in Neverwhere came out of the budget special effects cupboard in the form of 3M light reflective fabric and... black contact lenses.
Also, there's the fact that the stop-motion in the other world is ever so slightly off, especially during the circus scene. It's hardly enough to be noticed, but enough to be unnerving.
For the shots down the tunnel to the Other House, the two cameras used to get a 3D effect were set a bit farther apart, warping the perspective enough to make you realize something was up. In other words, when you looked down the tunnel, you were seeing it through a pair of eyes that no human can have.
When Coraline is searching for the lost children's souls, and she goes into Bobinsky's apartment, Bobinsky is seen dashing around in the background. Anytime you see him, particularly as he's winding around the rafters, it seems like he doesn't have bones. The effect is profoundly unsettling.
Visual Effects of Awesome: About halfway through the movie, try to remind yourself that the movie is stop-motion and not CGI. No, you can't.
What Do You Mean, It's for Kids?: Yes, despite being terrifying, this movie is appropriate for kids, so long as they can handle a good scare every now and then. Oddly enough, the ABC Family airing slaps it with a TV-14 rating.
The Woobie: Coraline, the ghost children, other father, other Wybie, and arguably the real Wybie.