I admit that MobiPocket Creator is still my choice for dealing with PDF files that have necessary images. Most of the books I convert do not have images and for those I have found that using mobigen is excellent. Of course getting the pdf to mobigen is fun. So I use PDF2HTML. This has been great so far for most PDFs. I actually integrated this into a script along with some other document conversion. Its up on sourceforge. Its simple to use and its appropriate if you have an eReader that supports mobi format like a kindle for example which is what the program is named after but it just creates flat mobi files without images. Heres the link Enjoy
Project Page http://sourceforge.net/projects/autokindle/
Download http://sourceforge.net/project/platformdownload.php?group_id=248415