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.
Awesome Music: Pretty much their entire catalogue, although Ænima and Lateralus are generally considered their best work.
Epic Riff: ...and not just on the guitar. The bass intros to "Sober" and "Schism" are probably the best-known. It's pretty fair to say most Tool songs are built around an epic bass riff, with the guitar and drums adding a whole lot of texture and atmosphere.
Genius Bonus: Do you happen to be a kabbalah scholar, Conspiracy Theory nut, musician, possess degrees in psychology and mathematics, and have a passing familiarity with drug culture? All at the same time? At this point you may, unaided, begin to understand just how many, many obscure references and in-jokes Tool loads their music and lyrics with. Being genuinely insane may or may not also help. See Viewers Are Geniuses.
It's Popular, Now It Sucks: When Tool made their first steps toward popularity, some fans reacted with typical outrage, causing an obviously angry Maynard Keenan to fire back with the song "Hooker with a Penis," in which he mocks a typical fan for having ever "bought in" to his music in the first place.
Magnum Opus: Ænima is usually considered this. Sometimes Lateralus gets the nod instead.
Misattributed Song: For some reason, more than a few people think the theme song for Doom 3 is by the band. It's a very understandable mistake, but it's actually by Tweaker.
Before the release of the game, various sources claiming Tool made a song for it did not help matters much.
Even more misleading is the fact that there were no vocals in the song.
Mondegreen: Given the lack of official lyrics and the at times distracting background sound, it's almost inevitable even for the lines that aren't completely indecipherable. Check three Tool fansites about how lyrics to any given song go, and you'll likely receive between two to five answers.
Nightmare Fuel: A lot of their videos, a few of their songs, and arguably the entire Lateralus album.
Reclusive Artist: Maynard, primarily because he hates how famous musicians are deified and also because he's not particularly comfortable with fame to begin with. This has, among other things, resulted in him chasing stalkers off his property with paintball guns.
Tear Jerker: "Wings for Marie/10,000 Days," seeing that it's an emotional tribute to Maynard's mother from Maynard himself.