There's only one way to memorize the fretboard and that's tons and tons, and years of practice.
You can simplifiy things to a certain extent by learning 3 note per string scales and rock scales in the most used keys for guitarists.
In other words... most guitar players tend to deviate to playing tunes in A and E. Mainly cause they're the easiest tunes to to use open strings on.

If you learn all your scales in A and E and get used to finding your way around the fretboard in those keys, you've won half the battle.
Anytime you hear a song being played in E, you know automatically that all you have to do is go up the the 12th fret to play a rock scale and it'll fit.
You can play an open E to give it some bass, you can play E chords with the E and 1st and 2nd strings open almost all the way down the fretboard....
You can hit strings 1 and 2 on the 12th fret and get a harmonic....

Once you get used to doing those keys, you can gradually move around to other notes like G. Where you can play the 2nd, 3rd, and 4th, notes at the 12th 7th and 5th fret to get harmonics....

Try learning these scales first and just move them up a couple of frets at a time until you get used to changing them around.

http://www.guitartricks.com/2000/trick.php?trick_id=3050&s_id=28