Suddenly the pickups closer to the fretboard have lowered themselves and it started to look weird, because one pair is close to the strings and the other one inside the body, so I thought I should adjust it. What's the key to the best sound?
Fret the strings at the highest fret (High and Low E should be fine for measurements), and set the pickup to be about 1/4" beneath.

I think generally higher pickups means they will be louder but lower down means the tone will be clearer, it's just a matter of taste really.
The key to best sound is:

1- Plug in guitar
2- Turn on amp
3- Adjust pickup height
4- Listen

If you are not happy with the sound you get from step 4, repeat step 3 through 4 again
^ Agreed.

Generally when setting guitars up, I try to use 1/4" as a basis, and adjust according to the player's style.

Last edited by deftonesordie at Mar 11, 2009,
But do high pickups mean noise too and easier harmonics? Because I don't like them very much...
No, that's pickup placement in relation to nodes. (WHOOOOLE other issue)

Just jam for a bit, have a screwdriver handy to adjust the pups, and move the pup up or down every so often and see if it makes a difference for you.