First and foremost, much of our tone is in our hands. Even the best gear can only serve you as well as you can control it. A lot of tonal variation comes from where you pick the string along its length. Near the neck pickup gives the most volume and bass because the string is more free to vibrate in the middle. Picking near the bridge results in a brighter sound with less volume and bass. Because the string is fastened there it cannot vibrate as intensely. This little wonder of physics means you can control your volume and tone according to where you pick the string.
Eric Johnson picks up on the finger board to imitate a Japanese Koto sometimes. Another thing he does is pick directly over the harmonic of the note he's playing. This gives a great octave effect. Speaking of harmonics, there are many ways to generate them with your bare hands, your pick or a combination of both. Any given tone on the guitar has a whole series of harmonics contained within it. To hear the harmonic series of your open E string pick back and forth rapidly with your right hand while your left hand travels from the nut to the bridge touching the string very lightly.
Its really amazing how many sounds can come out of a single note. Stay tuned and next time I'll disclose the secrets I've learned that help me generate harmonics in a wide variety of ways and flavors. Here's to your continued experimentation and learning.