I have my entire ebook library (about 3,500 volumes) on my PDA, mostly because I
can. The library takes about 1.7GB, spread across two 2GB cards. (My PDA has two SD slots, so both are available at all times.)
The primary store in on my desktop, in an \eBooks directory on a secondary drive. That directory is 11GB, with 49,00+ files in 3560 folders. IT contains source files in a variety of formats, plus conversions for the PDA.
By preference, I get HTML source files, and convert for the Plucker offline HTML reader for Palm OS, but I have files in MobiPocket, PDF, and other formats, too.
Books are stored by category, the by author withing category, and then by title. I use a naming convention for books on the PDA to make things easier, because Plucker doesn't support folders on the card. It assumes all documents are in one folder, and have been assigned a Palm OS category. Palm OS has a limit of 16 categories, and fitting everything into them was a challenge. I wouldn't mind more categories and finer grained control, but I can deal with what I have.
On device (for files I create), I use a naming convention of <Author's Initials> <Series Number> <Title>, so David Weber's Honor Harrington series, for instance, will have book titles like "DW HH01 On Basilisk Station" in the SF/Fantasy category, and the list will display by author, and then by series and series number (if any) in the list of books in that category.
MobiPocket files are stored similarly, though Mobi substitutes Reading Lists for categories, and can have up to 32 lists.
The PDF viewer I use supports folders on a card, so I can organize PDFs by folder, but by preference, I don't use PDFs if the book is available in any other format. Reading a PDF on a handheld device can be a painful experience.
The biggest problem is the need to maintain multiple viewers to handle all of the content I have, and recall which book is in which format read by which viewer. I don't see that changing any time soon.
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Dennis