Guitar Basic Music Theory

For the purposes of this article let me assume that you've taken the first step towards learning theory and learnt where all the notes are across the neck. If not, then you should do that first. Knowing the notes is extremely important to start applying theory.
The first thing is to learn scales and how they are put together starting with the major key, let us take C major.
The major scale is made from seven different notes. The first note is called the root note, the note that you start the scale with. The root note is where the scale gets its name from. In this case the root note is C, and so the scale is C major. Each fret on a guitar is a half note, or a semitone. To play a major scale go up the neck in the following increments;

Root, whole step, whole step, half step, whole step, whole step, whole step, and then a half back to your root one octave higher. The third note in the scale is the note that decides whether it is a major or a minor scale. In a minor scale the third note is one semitone lower in pitch than in a major scale. Try playing it to hear the difference. The notes in a C major scale you should notice are; C, D, E, F, G, A, B. See a pattern? There are no flats or sharps in the C major scale, which is why C major is easy to start there when you begin learning.

The next step takes a lot of time and a lot of practice. Take these notes and find them all over the neck. Try to learn the scale in as many places as you can, make sure you get really comfortable with it. You'll find that once you're totally at home with the C major scale it should be quite easy to move the shape and patterns around to find other scales. Try moving every note you know from C major up two frets on the guitar. You're now playing the D major scale. Move one half step down from C major and you're playing the B major scale. Take shapes and patterns you know and simply move them round the neck, learning each key one at a time. Over time you will learn which notes are the fourth note, the third note, etc. As you play more you'll get a feel of what notes are good to start and end phrases on, where you can bend to and just generally what notes will sound better over each chord.

The next thing  is to start learning the minor keys. Start, say with A minor, the notes are A, B, C, D, E, F, G. Notice anything familiar? The notes of A minor are just the same as C major. In fact, if you take the 6th note of any major scale and play the notes up to the 6th one octave higher you're playing the minor scale. So after learning the major scales you will realise that you knew all the notes for the minor scales as well. Obviously they share the same notes but of course, you need to phrase them differently when you play.

If you're looking to learn a minor scale then the increments are;
Root note, whole step, half step, whole step, whole step, half step, whole step and then whole again to the root note one octave higher.
There should be plenty to get you going here. Ideally after some practice you should feel comfortable jamming in any key. Best of luck practising and remember that slow and steady wins the race.