There is also PDF Studio (windows, mac & linux). Standard version $60, Pro version $95.

http://www.qoppa.com/pdfstudio/

I've played with it a bit and it seems to be very good. A fairly robust software. It's shortcomings are:- no ocr and it can't optimize. It only saves in the same pdf version of the file you are using. It's the only third party editor I've found that does bookmark/toc other than Acrobat Pro. (I use a mac). One of it's advantages is:- it is capable of exporting and importing annotations in .fdf and .xfdf formats. This is something I wish Entourage would implement. It would be huge. It would mean we could move our annotations to a pdf file on a desktop application and save them. Acrobat Pro does this as well.

Regarding the optimizing, I am looking at a small software that is made to do this.

If you just want to create a TOC within the Edge Reader, you can hilight the Heading you want, but then you have hilights in your text. If you don't want a markup to show, you can select the pencil tool, choose white as the colour and underline the heading. The drawback to this is that you would have to key in a title in the annotation dialogue box. Pretty labour intensive.

Neither of these methods are heirarchical and will not migrate with your file if you remove it from the library.