Again, I reply with use what works for you, but think it out thoroughly before you being...
A finely tuned file system is AS importantant as a well designed database schema... yet it is where people often go wrong right from the start...
The key is to have a full plan of the final project before you begin. You don't have to know every detail, but you have a firm plan about what will be included and generally how it will work... from this you can design a file system that best meets your requirements.
It is a good idea, as mentioned above to have some centralized locations for non-code files, such as images, flash files, includes, etc.... I have seen projects where they have image subdirectories, for example, in every directory where the pages need images, which is pretty much everywhere, managing these becomes a nightmare, seriously.... CENTRALIZE these sort of resources and your life will be much easier. Besides, it facilitates reuse...
Other than that, I have also worked on projects where ALL code documents were stored in 1 common directory, so there was no depth in the file structure... this had advantages and disadvantages, as does building a files structure that matches your site navigation and/or layout...
That is another option, MANY people promote building file structures that match your site navigation or system layout, or flow... etc. This sounds good at first, but it can lead to serious maintenance costs, especially when making even slight changes to site navigation or design...
I am NOT saying any of these is better or worse than the others, except to say keep the resources centralized, but I want you to understand the various options commonly used and know that it is important to plan this out, don't let yourself be led into building folders ad-hoc (as you need them) if you find this happening, you didn't plan well enough, try better next time ;-)
One other point that everyone should plan at this stage is the linkage of their contents... I mean the actual format the URLs will take... relative vs absolute URLs, etc. when one should be used, when another should be used... each has an advantage, and search engines often use this info to help rank your site...
Absolute links are better when moving the source page within your site but worse when moving the target page within your site. Relative links break either way, so they are always on the worse side... BUT if you have a complex file/folder structure you may have very long, complex absolute URLs and be tempted to swutch to relative...
One work around that I have used, is URL rewriting with mod_rewrite... You can simplify long URLs in a complex folder structure allowing you to keep those long URLs simple enough so you don't get tempted to switch to relative URLs...
Also, take advantage of PHPs enviornment variables to keep absolute URLs easy to write and flexible...
Honestly, I keep most of my code files in a limited number of folders... too few and it is hard to find the right one in a huge list, too many and you get click crazy trying to work with the code.... I try to strike a balance...
Peace,
