All thread used in my quilts is 100% cotton because of the damage polyester thread can do to the cotton fibers of a quilt over time.
For piecing: 60-weight, 3-ply, Presencia
For machine quilting: 50-weight, 3-ply, Presencia, 40-weight King Tut, 30-weight Sulky
I use neutrals, solids and variegateds, depending on the look I'm after. Be sure to use a needle correctly sized to the weight of thread you're using so things run smoothly.