I have some strong feelings on this topic, so apologies in advance for the longish post.
Here's how I organize my audio files: I don't! Before you throw up, let me explain…
What I mean is that I don't sort, file or otherwise organize my audio files into folders in my operating system. Not at all. My entire working sound library is nothing more than several bazillion files living inside one single folder on my computer, I barely even give them names any more. Most still have the default generic name from whatever device or application they spawned from. "file0483.wav", "Reaktor52-28983.wav"
Heh, I bet there are a lot of people who are getting increasingly agitated by this. Contrary to how it may sound, I am actually a hyper-organized person, and I do have a great organization system in place. But over many years of using and designing custom media databases, I came to understand that audio has many inherent qualities which prevent it from being organized in the same way as, say, text files. Here's why…
Audio is too alive
There are several good reasons, but the biggie is: Audio is not always one dimensional. What good is your "Nature/Animals/Jungle/Birds/Parrots/Macaw_Rainforest_Morning_Take_15.aiff" filing convention, when that file also clearly has the sounds of 20 other types of birds, a fan boat, some chainsaws, a bunch of tourist chatter, and a thunderstorm in the background? A really awesome thunderstorm.
Why force yourself to make boring administrative decisions about where a file lives on your computer, a decision which may inevitably hinder its usefulness later, depending on where you decide it should go at that moment? Your computer doesn't know what that file is. It doesn't care how awesome the thunderstorm is. It's just a file.
It's creatively restrictive
In a pinch, after 14 cups of coffee, you've decided that the cool synthy stabby thingy file should live in your "Instruments/Synth/Analog/Leads/" folder. Great. But I think we all know that any one of us could take that little bloop sound and transform it into an epic pad or soundscape, or a bass, or a whatever. Point is, organizing the actual files themselves does little more than limit your use of them.
It's an artistic hindrance. You are an artist, but there is absolutely nothing creative or artistic about naming, sorting and moving around files. You are forcing your brain to bounce back and forth between left and right function, thusly sucking the creative energy out of yourself and eating away at your day.
Tag, in context
Sure, there are plenty of sound files that are just_one_thing, but your system should be flexible enough to accomodate ALL situations. Giving one file one name and sticking it in one folder forever isn't flexible. What is flexible? Tags. A file can only have one name, but it can have as many tags as your heart desires. Tags are clickable, searchable, quick to apply, short, sweet, are based on creative usage, require no typing, the list goes on. File and folder names are long, tedious, manually typed, manually sorted, and prone to human error.
Believe it or not, there is nothing more flexible than a single folder with a million files in it. As long as you use tags, and apply those tags in a creative context. What I mean is, applying simple and meaningful tags to your audio files WHILE YOU ARE USING THEM creatively. < This is important. There is nothing more lame or prone to bad decisions than an all-night file organization session. Instead, apply tags to files while in use, while the juice is flowing. Clicking on a handful of tags while you are doing some real work takes a few seconds, and will result in far more meaningful context than at 3am when you are playing file clerk.
It doesn't matter what tools you use. Soundminer, Snapper, Monkey, the plain old Finder, iTunes. Makes no difference. I've used every pro audio database out there, and designed several custom ones of my own and for others. My tool of choice these days is AudioFinder. It's a little on the ugly side, a bit bloated, but auditioning and searching are fast, and it has some editing and batching functionality that I've grown to enjoy using. It also has an excellent tagging system, and it applies those tags to the files in OS X as Spotlight comments. That means I can take that big fat folder anywhere, and with a few scripts I can get my entire tag system into any piece of software I choose and move on with my life.
Don't get me wrong. If I need to deliver files to anyone else on earth, I will name them and put them into a nice folder for people. Hell, I make sound libraries for a living. Those final products are neatly named, given metadata, etc. But during the time leading up to that final product, I am focused 100% on creative output. That is largely made possible by the low administrative overhead of my system. My non-system system, which happens to be orders of magnitude more productive than any other method I've seen or used.
It takes a lot of fortitude to cut the cord and just go for it. But once you do, it's really quite liberating, and is really much more conducive to creative work. I've helped others transition from some really massive directory-based systems over to this way of working and they've all said the same thing. They all love it.
You are an artist. Do whatever you can to keep your brain in creative thinking territory. Organizing files is the antithesis of that. Just my 2 cents.