One of my least favorite activities is organizing digital files. I have photos, ebooks, music, some videos and an overabundance of digital scrapbooking supplies, in addition to whatever files I create and save.
I mostly manage using the Windows file structure and organize all my media that way. For my books, I sometimes use Calibre to try to sort my books all in one place, but Calibre isn't intuitive to my workflow and I get frustrated with it in a short time and exit out.
Honestly, the (discontinued and unsupported) Sony Reader software works the best for me as far as organizing my books; these days they all go into there, and I use Calibre when I need a conversion. At some point I'm going to replace my computer and I suspect I won't be able to take the Sony software with me; I don't know what I'll do then. Learn to get along better with Calibre, I suppose.