iBooks works with PDFs. Load them into iTunes (File> Add to Library) and then sync to the iPad. In iBooks they will show up when you push the button for PDFs.
If you are using iBooks you can save a .PDF from an e-mail into your iBooks library or if you use "Dropbox" you can drop the .PDF into Dropbox on your computer and then retrieve and save it from your iPad. Both of these methods save the aggravation of having to "sync" to get the .PDF's onto your iPad. To save Word documents Goodreader is a good choice since it creates a file structure inside this app.
Thanks guys, this has been very helpful. (I'm not sure I understood aobama's post, but he's more of a newby than me - so that may explain it - and it's been taken care of now anyway.)
I too go with gooodreader especially as it has a fast windows downloader for the ipad which doesn't require you to log into iTunes.
Look for goodreader usb.exe a free download from their website.