First, you might get some more interesting replies on the calibre forum.
What I do is to use the file handling functions built into the OS and organize my library
by folders. Now, one reason for that is that my ereading device is also setup to handle
folder, subfolders, and files.
I have ordered a Kobo Aura HD which appears to use a different approach. So, some
consideration must be given to how you will need your ebooks arranged for your device.
The same is true in relation to how the device will handle Metadata, including if it is used
to sort the ebook listing.
Due to my devices restrictions in file naming conventions and to facilitate changes in a
large directory of files, I have found the free "Oscars Renamer" utility to be of much
value.
http://www.mediachance.com/free/renamer.htm
Luck;
Ken