GuitarCourses.ws Fretboard Trainer
Even if you do know the basics of music theory enough to be able to build major and minor scales from any given root, you're still far from being able to accompany a song on your guitar if the way you navigate your fretboard looks like 'So I've picked the D string on the fifth fret, which is a G... now I need a perfect fifth upwards on the G string, which is... one, two, three.. the seventh fret.'
This piece of software will help you get familiar with the guitar fretboard and learn to locate individual notes as well as whole scales swiftly. It provides a set of lessons on the five root shapes (C, A, G, E, D - all based on the five basic chords), which help you get root notes on all six strings from a given root note on any string. Then the program teaches you how to use this knowledge for finding practically any note on the fretboard. The last set of lessons is dedicated to Diatonic scales, both major and minor, so that you can learn the fingering and play solos without even looking at the fretboard. To help you consolidate what you've learnt, all lessons are supplemented with corresponding exercises.
There isn't much more to the program than that. The appearance of the virtual fretboard is mildly customisable, the explanations are clear, and there is even a bonus lesson (on Pentatonic scales) to get after you register your e-mail address in the program. On the downside, the program only deals with the standard tuning (EADGBE), so if you prefer to play in dropped D, or open D, or something exotic like DADGAD, you'll have to figure out the schemes all over again on your own or find another program. I personally would also welcome some fingering technique lessons and exercises as well: this would make the program a bit less virtual and encourage users to practise the approaches they've learnt on a real guitar. Still, as a theory teacher, the program works nicely.