Both versions of GoodReader have been updated this past week, and I heartily recommend that you buy the app. It’s worth the $5. I got it a couple months ago, and then I stopped trying PDF apps for the iPad.
Anyway, the latest update adds a number of new features, including tabs (so you can have multiple files open), more annotation options, a couple changes to the navigation, a save file for PDF passwords, and other improvements.
I really appreciate the tabs, and the rest is just icing on top. To be perfectly honest, this app is so feature rich I’m still finding neat new things a couple months after i bought it.