On my HDD, I save my books in a folder structure, which also contains part of the total book-data.
LastName, FirstName\Series\Series Index - Book Title.
For saving to my various devices, I have as many save templates (using Calibre for that) as I have devices
Non-meta-data reading devices (such as my BBMini) use the same structure, my JE100 I use the meta data where the title is made up like this:
LastName, FirstLetter - Series - Series Index - Book Title.
And on the sony I use
Series - Series Index - Book Title
With collections of the authors.