Open the CITIES file with Paint (or a similar program) and change the civs colours (circled in red in attached image). Save the file and reload the game and you will see the changes. I cannot remember which is which but one changes the city name and one changes the shield colours. Every time I need to do it I have to work it out again
There are actually three tribe colour pixels for versions MGE or less. See this post.
There are two in Test of Time. See here.
In case you're asking about something else entirely: in versions MGE or less, you have a choice of 192 colours from an 8-bit palette (the one from units.gif); in ToT you've got 32 768 colours (15-bit Highcolor). Making major edits to the 8-bit palette is not recommended.
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