I am honestly very curious about what file structure you use for your ebooks. After 500 or so, I threw up my hands and just wrote some Perl scripts to flatten the filenames into something meaningful, and threw them into a big git-annex repository.

I have at least two dimensions I'm dealing with: title, and file type. Really though, it's nice to also organize by genre, and year.

I also dislike most of these walled garden library apps, and they are usually poorly written and obtuse. I would love an app that can scan my existing ebook repo, and then also create an index database, and make the books available on my mobile device.

One pattern for sharing my rigidly structured data from my desktop to my iPad, is to just share my working tree over Dropbox, because I use git-annex for my file collections. That way, I have automatic syncing of the files, but also the safety of snapshots. If I do want to incorporate a change I make on a mobile device, I can simply make a commit on my desktop, but if some poorly written app decides to start screwing with my metadata, I can re-check the files out. OSX Preview.app is infamous for this.