There are two main things to consider when it comes to colors and usability: colorblind users and color psychology.
Colorblindness refers to the difficulty in distinguishing colors from each other. It comes in many forms, and affects approximately 7-10% of the male population (much, much lower for women). UX Matters has a wonderful post about the different types of colorblindness, how they affect people, and things you can do to make your interface more usable for those affected. ColourLovers also has an excellent link about different ways you can provide feedback/information to the colorblind without taking anything away from the sighted in terms of color.
When it comes to color meanings, there are a ton of references and ideas about the impact of color on the viewer. It's somewhat of a hot/open topic in Psychology. Many studies have shown significant impact; many have failed to do so. It probably won't make a huge difference to your interface, but it's always something to take into consideration.
In your specific case, using a different color could speed up comprehension/understanding when creating and reviewing, but the effect would need to be learned by the user - there aren't any well-established patterns for color in that case (i.e. unlike red->stop/green->go). You might want to look to Quartz Composer for inspiration (different colors for input/output/generic patches)