I always use clear monofiliment thread on top and an Ecru-colored thread on the bottom of my free-motion quilting. I always pick backing fabric that the Ecru thread will blend with. (If you can't see my stitches, the quilting looks fabulous!) All of my piecing is done with the same neutral beige/grey thread.
Three kinds of threads in the same colors... that's it. I'm too cheap to go out and buy different colored threads to match each color of fabric in the quilt.