Hey!
I dont have anything really specific to recommend, what I did was just buy a book on general music theory and I read it page by page and tried to absorb as much of it as possible.
It depends on what your goals are: if you just want to play rockguitar in a band and (play cool solos!) you only have to know some basic scales like pentatonic/blues scale, the major scale (plus its modes), the harmonic minor (plus modes), know how to arpeggiate triads and maybe also 7th chords, and also some harmony that shows you how this stuff relates to chords.
If you want to get into jazz/fusion you´ll need to really REALLY know that stuff inside and out. If you wish to compose a symphony then theres a whole lot more you need to know.
My advice is to hook up with a good teacher who can show you how the theory bit relates to the music YOU want to play. That way it will all be useful to you, and then you can expand on it if you choose to. Also...TRANSCRIBE! Learn you favorite licks, solos and songs. Dont use tabs! EVER!!!! Pick em out by ear. Then the theory will be there and put names on the things you really like. Cause thats all theory is: names put on different ways to group and organize notes, just so you can learn them quicker.
Good luck!