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.
Crowning Music of Awesome: 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.
Fan Dumb: Tool has garnered an extremely passionate fan following, causing many fans to go way overboard in their adulation of their idols, which the band has always treated with open distaste and embarrassment.
Genius Bonus: Do you happen to be a kabbalah scholar, conspiracy theory nut, possess degrees in psychology and mathematics, be a musician, 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.
The songs "Wings for Marie, Part 1," "10,000 Days (Wings, Part 2)" and "Viginti Tres" are not finished. You have to sync "Viginti Tres" and "Wings for Marie, Part 1" with "10,000 Days" and play them at the same time. The result is one of the most terrifying and disturbing pieces of music ever conceived.
Suit yourself. Sure, it's slightly creepy, but its sheer awesomeness overshadows that by far.
"Faaip de Oiad."
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.
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.