In the file menu there is the option preferences and you can open the preferences .txt file and search for "color".
From my file
Line 57: preproc.color_datatype=true
Line 64: preproc.web_colors=true
Line 71: run.present.bgcolor=#666666
Line 74: run.present.stop.color=#cccccc
Line 75: run.window.bgcolor=#D4D0C8
maybe one of these will do what you want.
important to note is that you must change this preferences.txt file after you closed all instances of the IDE otherwise the file gets overwritten again.
ANother option is to tweak the Theme:
for my 1.04 version it is C:\Program Files (x86)\arduino-1.0.4\lib\theme
do not forget to backup these files before editing 