The GoodReader is 99¢, but the iBooks app will also do PDF's.... and its FREE. All you do is open iTunes (makes sure its the latest and greatest - v9.2.0.61) and click on Books on the left side of the screen. Now open your Explorer (This is in Windows. I don't know how to find files in a Mac.) and locate the files you want to copy. Now you can either drag the file from your Explorer window to the Books window or just copy & paste. Sync your iPad and voila... you now have PDF's! I just did this and if a Windows person can do it, how hard can it be???
Frankly, I wasn't a big fan of the iBooks app... until now!