The best tool that's helped me, is this chart that I MADE and attached.
Making the chart, led me to understand, how chords work, WHICH chords work, why they work, what MODES are, and how they relate to each other.
Embark on the quest to learn HOW to build these same charts, and you will unlock the secret that you are looking for. (Maj7 chords, min7b5, Aolian, Dorian, intervals, etc etc)
The top fretboard diagram is the harmonic minor (or classical sounding) scale.
The bottom is the regular major mode (standard rock, country, pop) scale.
Just pick a note with your eyball, and play the patterns like a robot. Similar colors represent octaves.
That's right, pick say green on the bottom (big/low E) string , choose a random fret and start your pattern from there. Any fret. Green can be any fret. The only rule is that the bottom row of dots represents your bottom string, the highest row represents your smallest string. (Logical?)
Skip notes, skip strings, experiment. EXPERIMENTATION is your best teacher.
However, the Guitar Grimoire series has helped me tremendously.
[edit] Shit, Purge you beat me to the punch .. hehe.
This is the reason I'm recommending it to you.
I own the Chord Encyclopedia, Progressions, and Scales and Modes.
http://www.guitargrimoire.com/