Shawn Graham just put up a nice post over at Electric Archaeology, in which he impliments some of my Skim–Markdown scripts. If you have had any trouble with those scripts I suggest looking at his post since he explains in more detail a few things I didn’t.
(By the way: PDFtk does run on OSX as a command-line tool called PDFtk Server; the GUI is Windows only. I use this in the apple script just to pull out PDF bookmarks, which I use for chapters in books, and make these headers in the resulting markdown —very useful organization for 300 pages of notes. As Shawn mentions, the script runs fine without this, however.)