All Animation Is Disney: Besides being mistaken for a Disney movie, it is also sometimes mistaken for a Don Bluth movie, which it isn't. Its posters and trailers which proudly proclaimed "from the creator of An American Tail" would have you think otherwise.
It's one of James Horner's prettiest scores. "The Forest" is a prime example.
Big-Lipped Alligator Moment: The part where the group comes across the flock of birds, and has to save Bosworth. This section really doesn't contribute anything to the story, except to introduce the concept of "the Yellow Dragons."
Also Edgar, who was the only character to get a limited edition stuffed animal version made.
Fridge Horror: Cornelius and his younger sister, Michelle's mother, narrowly escaped the gassing that killed their parents. Years later, the sister met the exact same fate.
What's more, the audience is shown the flashback involving the younger version of Michelle's mother just minutes after she dies.
Fridge Logic: Waggs is such a Jerkass because...well, imagine growing up with a name like Waggs.
Inferred Holocaust: Though two deaths (Michelle's parents) are shown onscreen, the gas leak would have probably killed many more cute furry forest creatures than that...
Nightmare Fuel: The music becomes a lot scarier after the gas leak from the truck spreads into the forest, but this is taken Up to Eleven when a freaked-out Michelle runs off and eventually makes it into her house which is full of poisonous gas causing everyone to panic and Abigail runs in after her. Now keep in mind that Abigail is a young girl going down an underground passage full of deadly gas and when she finally makes it to the bottom, what's the first thing she sees? The bodies of Michelle's dead parents. This is all while trying to reach and move her younger friend to safety, because she had been poisoned by the gas and was now unconscious and close to death herself as a result, all the while trying to keep her mouth covered so she doesn't inhale any gas too. This is why Abigail's bravery is so highly regarded by the others. This is a pretty intense scene for a G-Rated movie.
The scene with the owl counts for this all too well, with Abigail's surprisingly sharp teeth.
The scene where the humans return to clean up the mess, and Edgar gets caught in a trap. Luckily, it stops being scary when one of the humans frees Edgar and proves that not all Humans Are Bastards.
One-Scene Wonder: Phineas, the pastor of the bird choir, Willy and Waggs from the meadow.
Padding: The scene with the wrens sticks out the most.