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.
Nightmare Fuel: The music video of "Sadistic.Music Factory" in F. The song itself could be pretty scary if one takes into account the lyrics (which are about being trapped in a factory and forced to make music for a mechanical tyrant for the rest of one's life) and the frightening robotic monotones, but combine all that with the Chance Time ending...
Tear Jerker: The video for "Time Machine". An unseen person, whose viewpoint makes up the video, lives it up with the performer during the summer break, exploring the outdoors and building a scale model. It's pretty carefree... and then the cincher comes near the end where the person leaves on a train, and the performer's eyes tear up, and as the train pulls out, they run along with it, yelling along the way.
That One Level: "Sadistic.Music Factory" and "Negaposi*Continues" in F. The beat is fast and the targets come almost constantly. You have to be on top of the rhythm the whole time, or else you'll find yourself failing out very quickly.
Pretty much any cosMo song qualifies. In addition to "Sadistic.Music Factory" mentioned above there's also "Hatsune Miku no Gekishou" in 2nd and the famous "The Disappearance of Hatsune Miku" in the first game and extend (more so in the Miku Flick spinoff).
Tastes Like Diabetes: The inclusions and actions of the chibi Vocaloids in "God-Tier Tune" make it the most adorable apocalypse ever.
Woolseyism: Several instances of this in F. For example, one song that would literally translate to "Left-Behind City" was named "Urbandonment", and "Remote Control" became "Remote Controller", which is appropriate given the video has the Kagamines controlling each other through their devices.