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.
YMMV: Potter Puppet Pals
Crosses the Line Twice: Neville's death. Harry, Ron, and Hermione bully Neville to the point where Neville self-destructs. Not funny. But then they begin eating his remains, and it's hilarious.
Puppet Draco's death too. Draco getting decapitated and set on fire by Harry is a little too mean-spirited, but Draco getting decapitated and set on fire by Harrywhile Harry sings a happy song about what Draco likes? Hilarious.
Ear Worm: Any one of the songs. The most infamous is "The Mysterious Ticking Noise".
Harry sang the most self-praising I Am Song in "The Vortex."
Don't forget the Draco Malfoy song!
The birthday song from "Neville's Birthday" apparently proved so catchy, Neil released a video containing that song by itself.
"Funny Aneurysm" Moment / Hilarious in Hindsight: Depending on your point of view, "Stopper On My Pain", a song about Snape's "lost love", is probably one of these (Or a mix of both). The song, written long before Deathly Hallows, was actually supposed to be a melodramatic ballad about Gilderoy Lockhart. Through pure coincidence, it almost perfectly describes Snape's feelings for his real lost love, Lily.
Jerkass Woobie: Harry, to an extent. While he is a selfish jerk, his insistence about not having any tears over his deceased parents in "Ron's Parents" is a bit pathetically sad.