Reading PDFs on iPad without iTunes syncing
Put your PDFs in a folder structure on your computer, in DropBox, or on a computer somewhere online that you have FTP or SCP access to.

Then, in GoodReader, sync that folder. You can do it locally over WiFi and SCP or WebDav, remotely over SCP, or through DropBox.

Once the PDFs are in GoodReader, you can read them offline, mark them up, etc. If you set up bi-directional syncing, then when you are back online you can sync your notes back to your laptop.