I think what you are doing is an excellent...almost essential practice.
We have a "Shared" drive, a "Dept" drive and a "Users" drive (all mappings in the logon script). Shared has things like newsletters, logos etc that are to be available to anyone in the company. The departmental folders are for each department (with appropriate permissions) and the users folders are for their personal work. The vast majority of files fit one of these categories and this helps in finding and organizing work (particularly if someone is out of the office, etc).
Naming Convnetions are trickier...because some of that depends on your business and the kinds of folders you use. For example, when I worked at a Graphics firm, we used the Job Number and Client name as the folder name (ie J120122 - Johnson Cleaners). The preceeding job was the 22nd job done for the client and was started in December of 2001. This was relatively helpful when there were many many folders and much archiving.
Now the environment is very different and we tend to name things by function. For example in the Finance Dept (not called that for security reasons - but you follow my drift) there are folders for billing, expense reports, etc. They are organized by month and year.
While this is not a clear answer, what you need to bear in mind is what you'll be looking for and how you'll look. If you'll tend to know the customer, organize that way....if the date of the work, use that...if the product, use that.
Hope this helps some. Good Luck!
