Recently I've read a couple of articles here on how to master the fingerboard. While they are all good approaches, I learned the fretboard in a completely different way that I think might be of some help to you.
First off, I'm a completely self taught guitar player. The only lessons I've ever taken are on music theory from this graduate from Berkley. The problem was, that though he explained a lot of theory (up to the Harmony 3 level) to me, he didn't tell me how to really apply it. So I had to sit down with the guitar and figure it out by myself. I came across some pretty interesting observations that may be of help to you.
Now, from the very basics, we have the major scale. For simplicity, I'll use the C major scale though you may take any major scale that you already know/like.
The notes are C D E F G A B C(octave). The relation ship between notes is W W H W W W H, where W=whole step and H=half step. One half step is the distance between two adjacent frets on the guitar.
Once you're familiar with the formula, I would advise you to write down the notes of the major scale in every key. There are a couple of really interesting patterns that emerge if you do. I'll mention a simple one at the end of the article.
Now that you have the major scale in all keys, you can form chords from the scale. To cut a long story short, pick a note and take every other note in the scale to get the chord. For example, lets take C. Now if we skip D and choose E, skip F and choose G, we get three notes, i.e. C E G. These are the notes to the C major chord. If we had continued this, we would get C E G B which is the C major 7 chord. Continuing this, we get Dm, Em, Fmaj, Gmaj, Am, and Bm(b5).
All this is useless unless you actually apply it to the guitar. I strongly recommend sticking to the key of C for simplicity. Find the C note on the guitar. Its on the 8th fret of the low E, 3rd fret on the A string, 10th fret on the D string, 5th fret on the G string, 1st fret of the B string and again the 8th fret of the high e.
Next, find the next note of the C major chord. This note is E (major third). If you find the E note on any one of the A, G, D strings you will notice that its one string below and one fret to the left of the C note. So, if your C note is on the 8th fret of the low E, then your E note is on the 7th fret of the A string.
This interval (major third) is present in the same format on all pairs of strings except the G-B string, where its right below the root note. So if you take the 5th fret of the G string which is C, and you take the 5th fret of the B string, you get your E.
Now, you have two notes of the three note chord. If you move three half steps up from the major third, you get the fifth on the same string. This means, if we have E on the 7th fret of the A string, if I move to the 10th fret, I get G which is the Perfect fifth of C and the last note in the C major triad.
For minor chords, the move your finger one string down and two frets to the left of the tonic. The Fifth remains unchanged.
This is a lot to absorb and I'm sorry I can't give you diagrams right now, but take at least seven keys (C,D,E,F,G,A,B), write down their notes and then their chords. Then try to find the chords all over the neck by yourself. You'll come across a lot of interesting shapes and voicings for the chords and I promise you that you will never forget the fretboard for as long as you live.
Whats more, you now know the fret board, the arpeggios of all these beautiful chords and you have a very very solid understanding of the basics of theory as applied to the guitar.
Now, if you wrote down the notes of the scales, you'll notice that as you move up in fifths, each scale gets one more sharped note. For example, if you write the C and G major scales, you'll notice that their notes are the same except that the 4th is sharped (F# is present in G). Compare the G and D major scales and again you notice that the 4th is sharped in D major (C# is present).
Whats more, if you write the notes of all these scales next to each other, you'll see all the triads along the diagonals. There are 4 diagonals that you should be able to identify and you will find the notes of all the possible types chords in those diagonals.
Its a long article with a lot to grasp. There are a lot of other lessons available here on music theory, scales and chord construction. I've tried to keep it as simple as possible and hence I have not named the intervals etc.
I hope this has been of some help to you and that you gain from it. Happy plonking!