I'm a great fan of using a thread made of the same fiber as the fabric so that the thread and fabric will react the same way to cleaning and the passage of time. Sometimes I go so far as to use waxed ravelings for hand work to be sure the color still matches after the garment has been worn in the sun.
Linen and wool threads are hard to come by, and seldom suitable for machine stitching when found, so I sew linen with cotton and wool with silk. Keeping plant fibers with plant fibers, animal fibers with animal fibers, and synthetics with synthetics is more important than an exact match. Animal fibers are preserved by acids and destroyed by alkalis; plant fibers are the other way around, and every cleaning agent that whitens cotton yellows wool -- if it doesn't dissolve it.
Around here, all the readily-available cotton sewing threads are only three ply, which makes them too weak to trust for seams in garments that are going to be worn and washed many times, so I use cotton sewing thread only when I need to match a color. For seams where the thread doesn't show, or where I don't mind a contrast, I use six-ply crochet cotton
-- DMC's Cordonnette #100. The quality is enough better that I don't mind winding it off the ball onto spools. It helps, perhaps, that I have several 800-yard wooden spools, so I don't have to wind one very often. Also, I snitched a hand-cranked antique drill from DH's workshop, which makes the job go much faster. (Bobbins can be wound directly from the ball.)
Joy Beeson