In mathjax syntax you can can add colors (text, background or border, in fact any css elements) by selecting the mathematical notations you have written and then using Select text color and Select background color buttons/palettes in editor toolbar (or html). Mathjax also supports colors in mathml but only \color in latex expressions.
In my asciimathml script latexmathml was written to give full color support and it works nicely with combination mathml & mathtex fallback with \textcolor and \colorbox syntax but requires \usepackage[usenames]{color} or \usepackage{color} either in tex filter tex preamble or in fallback tags if color package is installed in that existing latex distribution. Again if I set asciimathml script to use mathjax fallback it can use in latexmathml (latex) syntax colors with all other browsers than IE6-8 that would require mathtex fallback...
Even if mimetex supports only a few named colors with custom syntax like \red, \blue or \green google chart api tex (that otherwise is using mimetex syntax) can use all colors + gradient & striped fills with chart api syntax and you can change both textcolor and background color in editor googletex plugin with color tools at the top of plugin - background is set to transparent by default.
Mathtran does not support colors at all - here some background from year 2009: http://moodle.org/mod/forum/discuss.php?d=133132#p587630
More about this kind of issues in the coming docs - it may take some time to get the docs finished...