Big-Lipped Alligator Moment: A minor example, but after Irene and Curdie have escaped the goblin caves, the first thing Irene says is, "Look, Curdie! The moon!" and both of them burst out laughing. It's as hilarious as it is random. Perhaps the reason of this is because seeing the moon assured them they are finally out of the goblin caves, relieved they then laugh.
Iron Woobie: Curdie. The poor kid takes a lot of punishment but just keeps on going.
The attack on Irene at the beginning of the movie.
There's also what the Goblins plan on doing to Irene herself. It's not simply a case of marrying her off to Froglip and forcing to her live underground. They also plan to cut off her toes because they find toes ugly (even though the Queen has twelve of them, so go figure) and keep a bag over her head at all times so Froglip doesn't have to look at her. And even though it's never brought up because this is a children's movie...uh, what happens AFTER the wedding? Yeah, ick. Kind of brings things to a whole new, way horrific level, doesn't it? One could be charitable and say Froglip would find her too repulsive to touch, but what happens when it comes time for little heirs to the Goblin throne? In the original story the Goblin Prince was half human so it is possible for goblins and humans to interbreed in this universe. Nightmare Fuel indeed.
Toy Ship: Irene and Curdie, natch. It helps they are pretty cute together and they each rescue each other in the story.
Values Dissonance: The reason Harelip's name was changed to Froglip. A harelip is a real deformity and naming your evil, ugly character after something like that would not have gone down well for modern day audiences.
Visual Effects of Awesome: The flooding of the castle in the film's climax because of how tricky and expensive animating water the traditional way can be.
The Woobie: Irene, arguably - her mother died when she was little, nobody believes her about the goblins or her great-grandmother except for her father (who is absent a lot, being the King) and the goblins intend to kidnap her and marry her to Froglip.