I've used the instructions from Sony about converting to PDF formatted for the Reader and I think it works very well. I've been buying my ebooks in html for a while now and I've set up a template in Word that I just insert the text into and then Save As PDF. Works great.
(Hmm, I just tried to locate the link for these instructions and the link on the Reader site is not there. It says Click here for instructions, but there's no link.
)
I should mention that the "author" in the properties needs to be changed (otherwise you'll be listed as the author of everything you convert).
Cover images need to be resized, too, at least in my experience. Easy enough to do, though, so the whole process is finished in a matter of minutes.
I do recommend it if you have access to the original (non-PDF) documents. If you only have the PDF, then I'd recommend Rasterfarian (correct spelling?). It's always worked very well for me.