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.
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.
Hate Dumb: There's quite a bit of criticism about the Green Aesop treating the humans as bad guys. Anyone who watched the movie knows that the humans immediately come back and clean up the mess the gas leak caused, and the gas leak is caused more by human carelessness than actual malice.
And even then, The human driving the truck CLEARLY SAYS, "Gas - I gotta get help!" before running out to get help - anyone would have done the same in his shoes! Stay behind, you run the risk of dying in the gas, too!
It largely has to do with people's knee-jerk reaction to anything with a Green Aesop, which is unfortunate when something that actually presents it reasonably comes along and is still immediately dismissed.
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 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's body to safety, because she had been poisoned by the gas and was now unconscious and close to death herself as a result. 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.
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.
The end of the movie where all of the families are reunited, and when Cornelius tells Michelle that though he can't ever replace her mother and father, he'll do his best to raise her.
Cornelius's backstory, where he reveals that his own parents were killed in a gas leak when he and his sister were furlings.
Values Resonance: After things like the oil spill in the Gulf of Mexico, this film and its aesop are still particularly relevant.
It stands alone as one of the unique western animated movies that aren't "princessmovies" with a female central protagonist, something much desired for nowadays and even more rare when it was released.
Cornelius certainly qualifies, especially given that now Michelle is all the family he has left in the world, and he can only sit there helplessly as she's slowly slipping away.
Also Abigail, when she starts feeling bad about herself for thoughtlessly leading the furlings into danger.
Edgar also has his moments of this.
Also Bosworth, the young wren trapped in the mud that the furlings save.
Unfortunate Implications: Along with part of Mighty Whitey, apparently the birds who know the land well and have wings cannot save Bosworth who is very slowly sinking, they just give up and have the funeral. But the kids who know nothing of the land and lack that Jive Turkey accent easily get him out.