I use invisible thread on some projects, mostly wall hangings, table runners etc. Invisible thread should not be used on baby quilts, if some of the stitches come loose it can get wound around baby's fingers.
On quilts I use coordinating or contrasting cotton thread. I like some of the variegated threads as well.
Whether I'm using invisible or cotton thread, I use thread the same color as the backing on my bobbin. :)