Set AltColor, a type REG_BINARY value name to the RGB (Red, Green, Blue) equivalent of the prefered color. Example:

white would be ffffff00. You would set this value at:

HKEY_Current_User\Software\Microsoft\Windows\CurrentVersion\Explorer

You can also set it at:

HKEY_USER\.DEFAULT\Software\Microsoft\Windows\CurrentVersion\Explorer

If you want to set it for each user, you can run regedit /s compclr.reg in a login script. Compclr.reg would contain:

REGEDIT4

\[HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Explorer\]
"AltColor"=hex:rr,gg,bb,00

where rr is the Red component, gg is the Green component, and bb is the Blue component.

You will have to logoff/logon for the change to take affect.

Here is a table of common colors:

 Color   Red   Green   Blue 
 white   ff   ff   ff 
 red   ff   00   00 
 yellow   ff   ff   00 
 green   00   ff   00 
 cyan   00   ff   ff 
 blue   00   00   ff 
 magenta   ff   00   ff 
 brown   a5   2a   2a 
 black   00   00   00 
 JSI burgundy   99   00   00