I set up a system before I downloaded Calibre.
I create a folder for each *source*. Thus I have a folder for MobileRead, one for Amazon, one for Feedbooks, one for Fictionwise, etc. etc. I make no attempt to keep the Sony books separate from the Mobipocket ones or even the .lit and .ePub ones -- the file type takes care of that for me.
Since the file name often doesn't contain enough information, I set up a spreadsheet which contains the filename, title, author, source, genre, and miscellaneous information.
I am a list keeper, so I have lists galore: books I read in 2008, books I read in 2009, books I want to read, series books I have read and need to read, etc. From my lists, I can generate statistics: percent of all books read that are mysteries, ratio of electronic books to paper books, etc.
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