I didn't really have an answer at the time since the thought had never occured to me. So I looked into it.
Popcorn on the whole is a low fat, low sodium, high fibre snack and can be quite healthy. Traditionally it's coated in fat, sugar or salt though making it less than nutritious.
From what I could gather, there is no significant difference nutritionally between types of popping corn. The only major difference will be color and texture. Some corns you might want to try include white popping corn which comes out almost snow white or traditional popping corn which comes out more yellow and anything. There is also blue, purple and red popping corns available but they are harder to find.
Most of the texture in popcorn comes from how you cook it. Cooking popcorn on too high of a heat will cause the shell of the corn kernal to pop before the inner starches mesh together properly, resulting in a tough centered popcorn. If you cook it too slow, it won't pop at all.
Overall, I think different color popcorns make for an interesting looking bowl, but they won't really improve the nutrition. The secret to great popcorn is all in how you cook it. See my parmasean, chive and garlic popcorn for a start!