I found a tip in another thread that helps. If you go into preferences and enable "Color Blind Help", each city on the map will show its nationality as well as it's name.
You can change them in game, but only by editing the files in your .../Art/Units/Palettes folder, which would get a bit confusing. If you want to change them for your regular game, go in your Civilization III folder, and select "Civ3mod" (or the equivalent in your PtW/C3C folder if you have them), then go to Scenario, Custom Rules, say yes to the warning, then navigate to the Civilizations tab, and in the bottom of the screen, you can change the colors each civilization has...not the greatest though, you are stuck with the same colors.
If you want new colors, you have to edit the files - the most common 'new' civ colors that are used are made by Rhye. They have really nice shades.
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