I agree with Mad Jew that the future is using Spotlight to find files, so organization doesn't matter so much, and also having a big folder with lots of folders and also hundreds of files doesn't sound too efficient for the "old" hierarchical way, (and iTunes is better at organizing MP3's)
two things:
If you're a web designer (or any kind of designer, really) you will have lots and lots of folders and files with the exact same names, and the most efficient and reliable way to segregate them is with descriptive folder names and hierarchical folder trees.
For example:
My company has 10,000+ products that are sold online at various vendors and through various distribution channels. We have product photos for these items that are formatted for specific purposes: web, thumbnail, print, the original "master" file, alternate images, etc. To maintain compatibility with the dozens of external databases that regularly pull from our networked resources, we need to maintain a consistent naming structure: UPC numbers are the files names, followed by the file type. Alternate shots get an additional "extension" between the file name and the file type extension.
example:
093849504938.jpg
093849504938.gif
093849504938.psd
093849504938.pt01.jpg
There are usually 3 different jpg versions of the main product image alone. They are divided courtesy of being in separate folders. These files are accessed by people using PCs and linux and mac OS and everything else you can imagine. We can't rely on metadata to easily search for upcs.
In 10.4, I had 5 shortcuts to folders set up in my left-hand finder tray, each pointing to one of the common folders (full-res psd, 600pixel jpg, etc).
When I needed to get a file, whether to place it in a document or to email it to someone, I would just search for the last 4-5 digits of the UPC and that would usually reduce the search results to 1 or, rarely, 2 items. In 10.5, they "fixed" this so that "filename" is no longer a default search parameter unless you type in the entire file name from the first character. (That's slightly off-topic, but it's completely broken now. Fix this Apple!)
The point is: spotlight searches are a LONG way away from being the organizational cure-all that you're proclaiming them to be. If they were so great, then we could have a single folder. Consider that folder locations and filenames are just metadata anyway. How do you think Time Machine works? filenames and folder locations are metadata and when you click on a folder and then on a sub-folder, that's the "search" you're doing. It would be nice to have that next level of abstraction in theory, but in practice, file names and folder locations ARE the search you need to do to get the files you want if you already know what files you are after.
If you're searching for a file and you don't know exactly what you need, just a general idea, then spotlight is great. styles.css searches in spotlight are generally useless, though. That's not going to change any time soon.
I've had my mac pro at home for less than 2 weeks and I already have 650,000 files in 137,000 folders on my primary drive, and that's not where I store my media and work documents (one too many corrupt system directory trees in my OS X past to do that, thanks.)
Thing 2:
iTunes organizes your files into folders and sub-folders the same way a lot of people would do it on their own. Clearly Apple thinks there is some benefit to organizing files into folders.
