You can change the colors of the messages displayed by various events, as well as changing the background color for channels or @listbox windows. Pressing Alt+K or clicking on the icon that looks like a row of crayons opens a dialog box for changing the colors.
There are 5 color schemes already created. I suggest clicking 'NEW' to make a new scheme name to play with, instead of altering the default colors then having trouble getting them back.
Otherwise, there are some colors like the titlebars which are defined by your personalized settings in Windows ControlPanel.