There's a wonderful little piece on how to use iTunes for organizing your PDFs (The complete guide to PDFs in iTunes).  

iTunes is an interesting beast.  It already handles music, talking books and your podcasts, and more recently video. PDF handling has been provided for some time, but it is not a very heavily advertised feature. You can organize, classify, rate - you can even get PDFs as podcasts.

It's not quite perfect - you cannot flip through PDFs you already have and have added using Cover Flow (at least, none of mine work that like that).