PDF reader that can save bookmarks & notes outside of the file

I usually carry PDF X-Change on my usb, along with some pdf books I need in my work, or something I like reading in between.

But the thing that buggers me is the fact that you cannot save bookmarks or leave pretty much anything related to a file without screwing up the file. So what I'm interested is this - is there somewhere out there a pdf reader that /like video players/ enables you to save bookmarks, leave notes and such, but doesn't save them in the file itself, but somewhere in its own directory. So you don't mess with the original file, but still have your way to easy continuing where you left.

Just for those interested, although hardly the perfect solution, this one is somewhat better then editing every pdf file in which you wish to leave a bookmark.

http://www.aldenta.com/2006/09/15/plugin-bookmark-a-page-in-your-pdf/

It is a plugin for Adobe Reader, and it adds an option in the toolbar, which enables you to save one (!) bookmark per file, usually the one which marks the position where you left off with reading. It saves the bookmrks information outside the file in the same directory where the plugin stands.

Although I'm still looking for a better solution, this works for me for now ...

You could have a look at Mendeley. I don't think it sync's bookmarks but it does sync notes and you can access these from any computer where you have installed the Mendeley app and from the web interface. I don't think it works for everyone but it really has changed the way I manage my PDF's.