Where are the pdf files on the iPad?
If they are in iBooks, sync with iTunes. If they are in a file sharing app (adobe Reader, Save 2 PDF, GoodReader) - then send them to iTunes within the app and then use the file sharing window in the apps tab of iTunes and you can drag them from the file sharing window in iTunes to your desktop or use the Save to feature.
You can also email the files to yourself and use DropBox. The DropBox app is free for the iPad and for the computer as well.
If the PDF files were purecahsed from iTunes, you can: from iTunes, select ipad> select apps> scroll down until you find the app containing your pdfs (goodreader, ibooks etc)> select the pdfs you want on your computer> click save to> and it will ask you where on your computer you want to save them
For the noe-purchased PDF files, you have to use third pary app like: iStonsoft iPad to computer transfer, or Amacosft for Mac user:
iStonsoft iPad to computer transfer:
Amacsoft iPad to Mac transfer: