hi stisev, i agree with you that calibre is a brilliant program.
in fact i use it exclusively for keeping track of my library.
however, you're also right that it might not be what *everyone* wants. if you want to organise your books without moving them or creating new copies of them, you might want to take a look at the
Harvey library management system developped by another member here, NetSlut. i believe it might be a more flexible system for you as it allows you to conserve whatever filing system / structure you prefer.
i don't think you'll get frequent updates like with calibre, since NetSlut has got quite a lot of other projects, and it's not meant to be a conversion tool nor does it have any other ebook utilities built in, however it does allow you to organise your library and it might work for your needs.
i hope that helps you.