FruduaTV: Guitar Repair and Setup This Italian luthier shows you great ways to get the most out of your instrument. Check out his method for stringing a Fender Stratocaster so that it stays in tune no matter how much you use the tremolo arm / whammy bar.
TuxGuitar This is a free opensource program that runs GuitarPro and PowerTab files. Great for learning songs.
JGuitar This site contains a bunch of useful tools including a chord namer, scale finder and chord calculator. Really handy for figuring out the official name of the chord you just made up.
Oolimo.com Another great online tool that helps you find chords, scales and arpeggios. Also includes theory lessons.
Music Discipline Enter the amount of time you have to practice and this site will give you a series of exercises to make sure you make the most out of your practice time.
My Color Music The official site for the Color Music System. A system for learning music theory with a special colour code that GTR is compatible with.