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.
Dr. Finklestein, Big Time. Did he create Sally to be his daughter? His Sex Slave? An emotional companion? A servant? All of the above? Who knows! And what of the mother-like figure he's with at the end?
Someone has said that he doesn't consider Oogie Boogie evil. That person? Tim Burton.
Oogie Boogie tend to get this a lot, often making Jack into a bully to do so. Also, Jack is probably one of the rare heroes (if not the only one) who gets this. Fans bash the military for shooting Jack down, despite the fact that they were justified in doing so.
Lock, Shock and Barrel have quite the popular fanbase, despite them being three homicidal, malicious, violent children. Although they do a Heel-Face Turn later...
Then there's Oogie's Shout-Out comment to Santa, sounding like Oogie's going to rape him.
The Show Some Leg scene! Seriously, that's probably the reason for the Oogie/Sally ship!
"Funny Aneurysm" Moment: The Mayor ends up falling down the stairs of Jack's house trying to get Jack. This is hilarious until you realize that the Mayor's voice actor Glenn Shadix died because of blunt trauma to the head following a fall at his Birmingham condo.
Jack himself looks like a distant relative of Slenderman.
Ho Yay: Of all the citizens of Halloween Town, the Mayor appears to be the most worried for Jack when he goes missing — and it doesn't look like just as a professional and/or as a friend, either. In his defense, there are only 365 more days until NEXT Halloween.
Ron the Death Eater: Yes, Dr. Finkelstein has a rather... questionable and dysfunctional relationship with Sally, but this does not excuse the Fan Fic writers for writing him into a freaking rapist.
Sacred Cow: Zig-zagged. Some circles hate it just because Tim Burton was involved, while others consider it the only good movie (Apart from Batman Returns) he was involved in. The fact that a lot of people grew up with it certainly helped.
Vindicated by History: It was a modest hit in 1993, and well-received by critics, but it wasn't near as big as Disney's in-house fare at the time (Aladdin arrived the previous year, The Lion King the next). This was partially because Disney was nervous about the Nightmare Fuel; they initially released it under their Touchstone Pictures banner (which was reserved for mature films and the edgier Who Framed Roger Rabbit). But now it's arguably a much more popular film than any of Disney's post-Lion King animated efforts, and they've since allowed it to be released under the Disney banner itself.
Visual Effects of Awesome: The entire movie is absolutely gorgeous, and there are some really creative designs to be admired if you look at the citizens of Halloweentown.
What an Idiot: No amount of naiveness can excuse Jack from actually trusting Lock, Shock, and Barrel to take care of Sandy and not hand him over to Oogie.
What Do You Mean, It's for Kids?: Several parents won't let their little children watch it because it looks too scary, while the actual film, outside of the kooky visuals and character designs, doesn't actually contain a lot which is unsuitable for a younger audience. It doesn't help that Disney deliberately moved Nightmare under its Touchstone label for the Nightmare Fuel, despite the fact that Disney has plenty of its own. But it was put back into the Disney label eventually.
All those who feel sorry for Henry Selick because he never gets credit for this film, raise your hand.
Sally. All the things she does for someone who doesn't reciprocate her feelings (at first) is heartbreaking. Though note that "not-reciprocate-Sally's-feelings" does NOT equal "hardly-notices-her".
Jack. A guy who gets tired of his job might sound whiny, but not when you consider that he lives in a town where it's all about said job. Put that on top of the fact that a lot of the responsibility for Halloween is on his shoulders, and all you have to say is "That's rough." Also since Jack is Dem Bones he might be Really 700 Years Old, who knows how long he was doing the same thing every year. 10 years? 50 years? 100 years? Since Halloween was created?