Tool always impregnates their art with depth and intrigue. And that's why I like them. I don't do enough syllable counting in lyrics, so if anyone can point to other examples of Fibonacci patterns in music, please leave a comment.
The only one that comes to mind is, maybe, Cymatics.
I was thinking of something else. I mentioned Debussy in another post (something to do with self-aware robots) and then later that week stumbled across something that linked Debussy & Fibonacci, but was thinking they were the same event. To your original question, wikipedia mentions Lateralus and a couple other examples you may enjoy:
http://en.wikipedia.org/wiki/Fibonaccinumbersinpopularculture#Music
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Off the top of my head I want to say Debussy, but I could be wrong. Didn't this come up in another post?