PDF manipulation software

[Rich Mahn]

I have dozens of PDF files containing a few thousand scanned images that I need to organize.
I am looking for suggestions for PDF software that will:
 -  rotate pages, groups of pages, or entire PDF files
 -  re-order pages
 -  move/copy pages from one PDF file to another
without re-imaging (or whatever the term is) so as not to degrade the images.

Also desirable but not necesary would be:
  -  the ability to add indexes/tables of contents
  -  annotation/notes as an adjunct on the page

What possibilities are available for Fedora?  or even Windoze?  (I can run
Windoze under a VM, or possibly even use wine, depending on the software.)