Like ChordMaster, ScaleWizard just tackles one aspect of the guitar (scales), but does a very thorough job.
Pros: Beautiful interface, tons of advanced parameters (arpeggios, modal scales, rare scales such as Semi Locrian b4). Landscape position offers full-screen fretboard view. Info screen includes options for left-handed orientation, alternate tunings, and automatic scale playback.
Cons: Not all-encompassing like Guitar Toolkit. Added background info or advice on scale choice would be helpful for novices.