Personally, I have organised my e-library as such:
c:\library\D\Drake,David\MOBI\Drake, David - Hammer's Slammers 01 - The Tank Lords.prc
So, I start with one directory for each letter in the alpahbet, then author, alphabetically by last name, Format of the e-book, and finally the file itself in my prefered naming convention which is Author - Series - Title
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