This first example is a peyote strip (a small one) with transparent gray beads at the top, and matte aqua beads at the bottom. You can see that by using white threads, the gray beads have an almost shiny, very bright appearance, and the aqua beads are lighter, you can also see how noticeable the threads are on the outside. Compare it to the next sample.
This is the same exact sample, but stitched with black thread. Do you see the difference in the colors? Just by changing the thread, I've made the gray beads a lot darker, and even the aqua takes on a more somber color. The upside to using the black beads in this piece is that the edge threads tend to fall away to the background and they don't pop out at you as much.
A good rule of thumb is to remember that bright threads will jump out at you and away from your beadwork while dark threads like black will recede into the background. However, be sure that you take into account how or if it will affect your beads. If these beads were opaque, the thread wouldn't affect the color at all, and I would only have to think about how they would look on the edges of my beadwork. Finally, here's a picture of the two side by side, so that you can see the difference. (Sorry, about it being sideways! Blogger has a mind of it's own!) Good luck with your next project, and remember...thread counts!