Guitarist's Reference ($5.99) is a very cool app if you want to know things like what scales to play over a particular root chord. In its simplest form, all you need to do to use Guitarist's Reference is tap the "Select Key" button and enter the root chord. Then tap the "View Recommended Scales" button and the fretboard populates with all of the notes from the chosen scale.
The app also includes triads, arpeggios, a reverse chord finder tool, alternate tunings and the ability to choose a right or left handed guitar.
The only thing I don't really like about Guitarist's Reference is that it doesn't work in landscape orientation. Since that's the way I normally use my iPad, it's rather inconvenient.