Make sure you have iBooks installed on your iPad/iPod touch/iPhone.
Open iTunes. Select File > Add to Library...
Now select Books from your iTunes Library. You should see the PDF file(s) there.
Right-click on the PDF and select Get info.
Select the Options tab. Make sure the Media Kind is set to Book.
Select the Info tab and add any missing data.
Select your iPad or other device from the Devices list in iTunes. Select Books from the tab list at the top.
Make sure your PDF is selected and then click on Sync.
Open iBooks on your iPad or other device and you'll see a PDFs button at the top. Tap it to open.