Well, I have a general Ebooks Folder
Within the folder I have books sorted like this
Genre - Author - Series - Books (all formats)
I've not settled on a single format yet, but am slowly moving toward HTML for storage.
What I usually do when I get a new books is to Strip off the DRM (as I buy Mobi), Create a HTML version and a LRF version. This way I have books formatted for all my devices while still having a universally usable format.
I'm still testing out creating other formats

, but that's mainly for the heck of it and not for any real need.
I also archive copies of the tools I use to format shift as well as any files and firmwares for my devices, Just in case