With the latest iTunes update, PDF files can be added to your iBooks reading collection through an iTunes sync. As the Simple Help blog points out, though, you can also just drop PDFs into your Dropbox space and add them from there.
Once your PDF file has synced and uploaded to your Dropbox account, search it out on your iPad or iPhone. Hit the "Open With" button in the upper-right corner, and select iBooks as your destination, and you're done. Of course, you'll still want to convert to ePub format if you want the full ebook experience, and want to read on other devices, but for simple PDF syncing, Dropbox seems like the path of least resistance—which, coincidentally, runs right around iTunes.
How to add PDFs to iBooks using Dropbox [Simple Help]