I think using the golden ratio gets you in the ballpark for many things especially visually. Wether it truly affect the sounds of an instrument if its length is phi times its width, I don't know, some people will want very hard to find it and cut corners to make it happen. It would be true if it would be the case all the time, not just with some examples, otherwise that would fall in the category of "you were lucky on this one". This page shows precise examples, with some comments being totally subjective, and it doesn't say if most saxophone mouthpieces of high quality, that would sound better than the one presented here, would have been designed with phi in mind. Etc. I would also bet the Speaker Wire patent shown below is pure snake oil, even the wording sounds very sensational. I don't say you couldn't improve audio signal with the phi number in mind, but most of the time, people are alienated with it and the placebo effect would do its job (especially in the hifi world)
Other than that, it's pretty much established you can find it in many fields, but a lot of what you would read about it on the internet is esoterism and myths as well. This page shows how BSy it can get :
http://www.goldennumber.net/golden-ratio-of-earth/ and how "I want it to happen" drives people interested in finding it everywhere.
EDIT : this one is not too bad either :
http://www.goldennumber.net/music/ The person who wrote the article wants to find the fibonacci sequence so bad that it lists things that have no relationship whatsoever so that he gets every number right. "there are 13 notes between a note and its octave" implying you count the note itself, plus its octave. If an octave was divided in 13, he would have said the same without counting the note twice, it would have been just has convenient. Then he says a scale is made of 8 notes which is only true for some of them, etc etc. Later on the page you can find some approximations he makes to get close enough to 1.618. I think it might be true you can find the phi ration in note frequencies but using approximations like this is not honest. There are 1 or 2 guys in the comment who pointed it out
You can probably find Phi in many things in audio theory. Starting from a rectangle room dimensions, I would bet on the fact the best rectangle room for a control room would feature the Phi ratio, or would be close to it
About Tool, you are mentioning the song "Lateralus", Maynar's vocal lines are 1 syllabe, then 2, then 3, then 5, 8, 13 and then goes backwards. In this case it's only a deliberate choice they made, I don't think you could say this song is awesome "because they used the phi number in it". You could add or remove a line and it would be just as awesome, and Parabol/a is as good as Lateralus and has nothing to do with the number Phi. Also, I think if you reorder the tracks of this album in the fibonacci sequence order or something like that, you get the "real" order of the tracks (with gapless transitions), or something like that. It's just an easter egg