The folks over at The Unofficial Apple Weblog have a handy guide up about how to get a PDF-formatted eBook running smoothly on the iBooks app. It's actually quite simple but before the most recent app update it wasn't possible to do natively. Now it's much easier.
1) Simply connect your iPad to your computer (either Mac or PC).
2) Then drag and drop your PDF eBook onto the Books icon found in the iTunes Library. This is a good time to edit the name and/or author of the books if necessary.
3) First click on your iPad or iPhone in the Devices list, followed by clicking on the Books tab.
4) Double check that the book title box is checked as well as the Sync Books field.
5) Click the Sync button. Voila!
TUAW estimates that most PDF eBooks should sync in a minute or two. And once you're done, iBooks will categorize all your PDFs together for easier searching.
