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.
Because of his insanity, whenever Batty Koda 'switches channels' he's clearly hallucinating in some form. The 'acid' parts of the "Batty Rap" could be interpreted as him seeing things, hearing voices in his head and speaking to himself.
Draco in Leather Pants/Evil Is Cool/Evil Is Sexy: How many fans feel about Hexxus. This is what happens when you make the villain more likable and entertaining than the rest of the cast (and have him voiced by Tim Curry). So much so that it's resulted in an accidental Broken Aesop; Hexxus is so much cooler than all the other characters he actually makes you root against the protagonists, and Toxic Love makes pollution seem so awesome it's probably responsible for spawning an entire generation of future Captain Planet villains.
Ear Worm: Pretty much every song in the movie. Toxic Love stands out because of the above trope.
A Dream Worth Keeping is a far more unpleasant, though fairly common earworm from the first movie.
Narm: The kangaroo mother's Skyward Scream in the second movie, where she drops to her knees while surrounded by flames and shouts "MY BAAAAAAABYYYYYYYY!!" The overly dramatic moment comes out of nowhere, and just looks silly with a cartoon kangaroo.
Listen to the full version of "Batty Rap" and let your imagination wander as to what Batty Koda must have been through in that lab.
"They used and abused me, Battered and bruised me, Red wires green wires stuck em' right through me!"
The scene where Batty sings that line about the wires always freaks this troper out. It's only about 5 seconds, but you see the wires glow under his skin, and he's making a motion like he's trying to rip them out (or slash his own wrist.)
One line from the uncensored version has a doctor directing people to remove Batty's skull cap. Just what were they doing to him!?
The most disturbing thing about the song is that what the scientific study was about is unclear. Several parts imply cosmetic chemical testing, but the wires and several other things imply seemingly pointless mutilation, and one particular line directly states that it was performed by graduate students, with moral objections no less.
"I don't care what you think you're a graduate student...JUST DO IT!!!"
Rooting for the Empire: Many watchers sympathize with Hexxus, who for the record is the incarnation of pollution in a heavily Anvilicious cartoon about how life is precious and pollution evil. He's an abomination whose end game is to kill all life, but that's what you get for casting Tim Curry as your main villain and utterly forgettable main characters otherwise (save for comic relief Batty).
Sequelitis: Take a baseline of Ferngully, then add the general degradation afforded to your average direct-to-video sequel, then remove the two things that were at all worthwhile in the first movie (a.k.a the voicework of "Tim Curry" and/or "Robin Williams"), add some horrendously cheesy musical numbers and you have a case of sequelitis with only one sequel.
Oh yeah and make one of the least likeable characters in the first film the main character and sideline the heroine of the first movie for most of it. Where can you go wrong with that?
Some Anvils Need to Be Dropped: Okay, so the movie was a little poorly conceived on the whole... but Batty and his rap are generally considered to be a legitimately good message because, in the decade prior to the film's release, a lot of the stuff portrayed in the rap was done to animals in testing (look up the Mary Kay Corporation's history of animal testing sometime - or don't, if you have a weak stomach).
Hell, the rap was censored in the theatrical cut because some of it was just too gruesome for a G rating, and it still squicked people out. In the uncensored song you can clearly hear the fairies gasping in horror as Batty tells them what humans have done to him, and his own screams in the background, most likely as memories.
FernGully tends to get some credit for inspiring some of the animal rights legislation later in the decade (having the bat voiced by Robin Williams undoubtedly helped).
Tear Jerker: Magi Lune's last words before she dies/fades away. Especially how she sounds... so grandmotherly.
I love you, Crysta...
Crysta restoring Zack to his normal size as it's very likely they'll never meet again.
Unfortunate Implications: Oh lordy, lots. To start with, there's the fact that the fairies live in the Australian rainforest... and only know about white humans. There are no aboriginals, a people they'd presumably be in touch with, to be found anywhere.
And for that matter, why are the fairies themselves white? Fairies in European settings don't look like aboriginals. (Usually.)
The style of the graphics in the intro, at least, implies that the original human inhabitants of Fergullly, the ones that fled Hexxus, were aboriginal. Since all that's left of them are some legends and (apparently) cave paintings, which are both abstract at best, there's not much indicator of physical appearance and skin colour for the fairies apart from "they looked a bit like us, just much bigger". As for the fairies' skin, well, they do spend nearly all their time under the shade of the canopy, being forest creatures. High melanin content is a trait of apes with open-air living and lots of sun somwhere in their recent ancestry.