Well, you could use Dropbox as a place to organize your library in any form you want and access it through your browser to download the book/magazine you want to read - limited just by the size of your Dropbox account.
If you already use calibre to organize your library you can use
calibre2opds which builds a nice html interface accessible through your Kindle browser.
If you don't use calibre, there is a script called
pyndexer which indexes your library and provides you access through an ordinary html index. This is the
thread on how to set this tool up.
Unfortunately the Kindle browser doesn't let you download PDF, MP3 etc. It's clearly done to minimize the 3G data volume. The only files you get to download are .azw, .azw1, .mobi, .prc and .txt.
There is no way to build subfolders on the kindle up to this time. And every time you add files a folder the kindle shows you all files which are not as yet in this folder, regardless of being in another folder already. This allows you to put your books in more than one folder (without having more than one file). So it's actually a virtual system of folders as you can see if you lookup the documents on your Kindle.