You can do it through coloring each of the metaballs through the point sop. After merging, the colors will even mix correctly.
As far as an output goes..you can render at the merge sop and render through the open gl rop (either as shaded or wireframe). If you want to actually render through mantra, you will have to add a shader after the merge. In the diffuse of the shader (i used a vex layered), put Cr,Cg,Cb in the fields. Then render with mantra, and voila, colored metaballs.
As far as having different textured shaders on each of the metaballs, that might be tough. Don't have a solution for that one yet and don't know if there will be one.
Here's an example file, if you're interested..
http://studentpages.scad.edu/~dquiru20/metacolor.hip [
studentpages.scad.edu]
Dave