Wire Color Codes
Although I've arbitrarily assigned various colors to the wires inthe schematics presented on this site, pickup manufacturers have their own systems.  They are consistent within their brand name, but within the market, anything goes!
Below are some of the most widely distributed manufacturers with their prefered color schemes.  For lack of a better system, the wires will be designated by letters corresponding to the coil and end from which they originate
A = Neck-most coil, left side
B = Neck-most coil, right side
C = Bridge-most coil, left side
D = Bridge-most coil, right side
The colors
 
Manufacturer
A
B
C
D
Seymour Duncan Black White Green Red
DiMarzio Red Black Green White
Gibson Black Green Red White
Schaller Green White Yellow Brown
Jackson Green White Black Red
Lawrence Black Green Red White
Anderson Red Green Black White

And then on most of these pickups there's also another wire that stands apart that represents the sheild.  This always goes to the ground.
Exceptions?

Note that several manufacturers are not mentioned here:

Fender doesn't seem to have any after-market humbuckers that I could find.

EMG pickups are anomolous in that they do not have traditional coils, let alone 4 conductors.  In fact, only their model 89 pickup can be "tapped," and that's by a specific scheme of more wires than is conventionally required.

If you see any brands I missed, please email me.

Single Coils
Thankfully, single coil pickups are fairly straight forward.  In general, the black wire is the ground side of the coil.  The other color can be almost anything else.  On Fender guitars, two of the non-ground leads are white, but the one from the middle pickup is yellow.  This is to designate that pickup as different.  Specifically, it is reverse-polarity and is reverse-wound.  This makes it hum-canceling when combined with either of the other two pickups.
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