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: Stella's song, "Come Fly With Me" in Wings Of Change certainly qualifies. Including sudden change in lighting and even background singers and dancers coming out of nowhere! Most of the songs are portrayed realistically (except Muru's in Wolf Quest, but he's a spirit so its justified), but hers...not so much...
Base Breaker: Star, Kaltag, and Nikki on whether they're funny or annoying.
Broken Base: The sequels are either considered surprisingly decent or plain bad fanfiction.
Draco in Leather Pants: Steele and Niju, despite being the Big Bad of their respective movies, are quite popular with the fanbase. Niju has the excuse of just being afraid of losing his home, Steele is a bit harder to justify. Still, doesn't stop plenty of fanfiction and fanart showing Steele performing a Heel-Face Turn and Niju paired with Aleu.
Steele was actually in the original script for the third movie, where he was supposed to help Kodi find Balto along with several others. He was left out for reasons unknown.
Ensemble Dark Horse: Star from the first movie. Sadly, he wasn't in the sequels. Same goes for Kaltag and Dixie as well.
Besides Kodi and Aleu, Balto and Jenna also had other puppies (named Dingo and Saba in the credits); we only see them like in two minutes of the second sequel (there's not even any consensus on which of the puppies is supposed to be who!), and yet they are very popular in the fan base.
Muk's famous entry quote: "Uncle Boooorrrrriiiiiss!"
Moral Event Horizon: Steele is an arrogant blowhard in the opening of the first movie, but he sails over the line into evil when he deliberately sabotages Balto and the sled dog team's efforts to reach Nome, thus endangering not only the sled team, but the dying children who desperately need the medicine being delivered. And all of that was simply because Steele was jealous of Balto trying to help Steele's team, and then forced to take it over as a last resort.
Ship-to-Ship Combat: Dear God, the fight between those who pair Balto's son Kodi with Dusty (who already has a love interest, according to the director of the second sequel and to her interactions with Ralph) or with Kirby is still going on!
Tear Jerker: Say what you will about Wolf Quest. The ending, where Balto and Aleu part ways over an instrumental "Someone Who Loves You", tugs on the heartstrings.
From the first movie: the little coffins. Granted, no one is actually dead yet, but that was such a horrible sight. To make it worse, the man making them is the same carpenter that made a sled for Rosie and was so delighted to see how happy it made her. Just thinking about how he must feel knowing she and so many other children might be buried soon and he's the one building the caskets...
They Wasted a Perfectly Good Plot: The sequels Wolf Quest and Wings of Change both present potentially decent father/child bonding narratives, but fail to live up to them in different ways. Wolf Quest has a good concept of Balto trying to help Aleu, but it's weighed down by the sudden inclusion of the rather complicated and unsubtle supernatural elements and interpretation of destiny. Wings of Change, on the other hand, seemed like it wanted to feature Kodi in a role akin to Aleu (Balto's fear of letting him down, Kodi wanting to make his father proud, the flashback to when Balto helped him as a pup, etc.), but ultimately doesn't fully explore the father/son narrative aside from a few key scenes (as Balto is the main focus, with Kodi in a supporting role).
The Woobie: Star from the first movie. It's impossible not to just want to hug him after Kaltag keeps hurting him. Its thankfully dropped at the end with a much needed smile from the latter.
Luk can also count, when he whimpers about Balto not coming back from his journey, and his brother reassuring him that he will come back not doing anything to calm him.
Iron Woobie: Despite all the turmoil Balto went through, he managed to go on a long and dangerous journey to get the medicine.