It seems I have just found a pretty good solution thanks to this post. The parts are:
- Calibre -"a complete e-library solution and thus includes library management, format conversion, news feeds to ebook conversion, as well as e-book reader sync features and an integrated e-book viewer."
- Stanza for IPhone - The most popular IPhone ereader.
I also tried the Stanza desktop app for converting the pdf and syncing it to my device. It couldn't open the PDF file and display it correctly for some reason.
I guess converting pdfs is still a fine art. It appears that for books targetted as ebooks, the Stanza reader will work out just fine and Calibre will do its job helping to keep it all organized.