Go to the apps section in iTunes on your Mac / PC (after you've installed iBooks) then scroll down, and you should see a box where you can just drag and drop things from Windows Explorer, or Finder.
once you have iBooks app installed, just drag the PDFs you want onto the iTunes icon. iTunes will automatically put them in the iBook PDF section and you will see a "bookshelf" full of them next time you sync the iPad.
My wife used to print out pages and pages of Real Estate listings to bring to clients, now she just prints to PDF, drags them to iTunes, syncs and goes out the door with zero papers. Clients dig it.
I'd have said Goodreader too. Especially for one-off files: love the wifi server thing. If you prefer iBooks as a reader you can always Open With for Goodreader. I love GR's PDF annotation though.
If you don't want to have to sync your iPad to transfer PDFs from your computer to the iPad, just use Dropbox.
Make sure you have the iBooks application installed on your iPad to view the PDF. Or you can use another app that let's you view and write over PDFs as well.
Then install Dropbox (free) and drag your PDFs into your Dropbox folder that sync wirelessly to your iPad's Dropbox folder. You can then view them in Dropbox or choose to transfer them to another place through the app.