I've used clear cups in the past, too, without any problems. The kind of more interesting thing is using "dirt cubes" - no cup or pot at all. With a clear cup, you can see the roots once they reach the edge, and they keep going just like they would if they were in an opaque cup. With "dirt cubes" (there's another name for them I'm not remembering), however, once the roots reach the edge of the dirt, they either turn back in or stop. Seems the open air is what they don't like.