What is a good resource for learning music theory, especially as it relates to the guitar, coming from a completely beginner's perspective? I had a musician friend try to teach me about modes such as Mixolydian, but I feel I should start far more basic, and I don't know what is most relevant to modern guitar music.
Check out Dave Weiners Youtube channel he covers all the modes there and a whole lot more, the Mixolydian lesson is particularly good as he applies it to multiple styles and explains why it works.
This guy tours with Vai and still finds time to make these lessons, awesome.
From personal experience: Piano theory lessons.
I started piano when I was 10 or so, and guitar when I was 17. I was amazed at the similarities. One of the things most people don't really think about is that they're actually both string instruments, of the "struck" variety (non-bowed, though of course you can "pluck" guitar strings).
The most valuable part to me was interval training. I was basically tone deaf before I did interval training, and now I can play a lot of songs by ear. This is really valuable with guitar since it's often when you can't find a good tab for a song.
A large portion of music theory is applicable across all instruments -- notes, keys, scales, etc. -- and an even larger portion is applicable across guitar and piano (all the above plus chords, for example). I wouldn't worry too much about getting into guitar-specific theory until you've covered all the basics.
In my opinion this is one of the best sites I have found. Simple, easy to understand, has examples and resources for practicing and memorizing theory, etc. I feel it also moves very smoothly from basics to more complicated subjects. I use it as my primary resource.
A good majority of the teachers that come into our store use Alfreds Esssentials of Music Theory. It does lend itself more towards the piano but its a wonderful series and learning that will only add to your knowledge and ability as a musician. It aslo gives the option of getting just the book, CD, DVD, or some combination of them all. http://www.alfred.com/emt
Another site worth looking at is http://www.musictheory.net/
They cover a lot of the basics and have some neat tools for re-enforcing the lessons.
The best resource may very well be a well educated teacher. One that can play you melody and harmony exercises for you so that you can hear what works and what does not would be especially useful.
Try getting one with a Licentiate and/or Diploma in theory. Also post grad work in theory from a good music school is a great qualification.
My teacher recommended Edly's Music Theory for Practical People. I've just started it. I find very readable and appropriate for a complete beginner. It has worksheets to complete in addition to explanations.
... learning music theory, especially as it relates to the guitar.
Coursera has free courses from music colleges / conservatories. They're growing too so I would expect new material over time.
Introduction to Guitar from Berklee College is highly rated by it's students and covers some foundational aspects such as major and pentatonic scales.
Fundamentals of Music Theory from University of Edinburgh covers a lot of theory and is very information dense but is also highly rated.