Lifelong fan here, enough to call them my favorite band of all time.
Saw them live 8-9 times, my 10th coming up in a few weeks.
It's funny, despite the 'prog rock' label, I always enjoyed Adam Jones' minimalist take on his guitar parts and sounds. He lets the band breathe. Danny Carey brings the math into the band, but it's so far away from any of the conventional prog rock that I have trouble listening to. Maynard is, despite his seemingly infinite capability for projecting his voice, a melodic, graceful virtuoso. And Justin Chancellor's bass, I would argue, is the single biggest 'signature sound' going in rock music right now. There is nothing like it.
Ironically, some of the comments that look at Tool's surface and connect it with 'society's decline' or whatever - it could not be further from the truth. Just spend some time with the Lateralus album. Try to get past the density, the noise, whatever you're perceiving that makes it intimidating to you. The whole album, literally, (laterally?) is about human progress- on a personal level, as well as as our species as a whole.
I'm also pleasantly surprised at some of the comments about Undertow being their best album sonically. Interesting- makes me want to revisit the album from that perspective. Undertow always sounded a bit 'naive' to me in its production, especially drums, ESPECIALLY the cymbals. But that 'naivete' does translate to a more intimate, (and arguably truthful) recording style as far as critical listening is concerned.
As the band's conceptual frameworks expanded, so did their sound, and the sound became 'bigger', which I enjoyed. Ænima still has some my favorite recorded moments of music in history. (The intro / first verse to "Eulogy"!). The sonic punch of "Lateralus" is hard to match by any other band on the 'harder' side of the rock spectrum.
Lastly - I've really really enjoyed the last album Fear Innoculum. It's a completely different beast. It will take years for people to truly digest it. I just keep nibbling on it.