I've not done much extensive research on the topic but from what I understand it depends on what you intend to do with it. I know that you can specify a second hotend in Slic3r to print support material (perhaps a soluble PVA) and there should be a likewise option in Skeinforge. Unfortunately though, beyond that there is not much out there for printing in multiple colors. The main problem is that you Slic3r cuts solid objects in an .STL file. There is no way that I know of to identify sub regions within an .STL file (in order to describe areas of different colors). I have heard of people manually editing their GCode to switch between printheads but this sounds like an absolute pain in the a**.
Not saying it isn't possible, but beyond using a second extruder for support material, I think we would need an entirely different workflow and host software to manage multiple colored extruders. I know this technology exists, its used in very high end commercial printers, but the models are designed and edited in proprietary software.
Do a couple of searches in the forum, I know this topic has been discussed, at length, by people a lot more versed in this topic than myself. Glad to hear that you are getting high quality prints already!