If you write the css file as an xsl template, you could read color values from a simple xml file. Then create the css with an xslt processor.
colors.xml:
<?xml version="1.0"?>
<colors>
<background>#ccc</background>
</colors>
styles.xsl:
<?xml version="1.0"?>
<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform">
<xsl:output method="text" version="1.0" encoding="iso-8859-1"/>
<xsl:template match="/">body {
background-color: <xsl:value-of select="/colors/background" />;
}
</xsl:template>
</xsl:stylesheet>
Command to render css: xsltproc -o styles.css styles.xsl colors.xml
styles.css:
body {
background-color: #ccc;
}