I like Presencia 100 percent cotton thread, 60-weight for piecing and 50-weight for machine quilting. I get very little lint build up from it. I also prefer to pair cotton fabrics with cotton thread. Poly is stronger than cotton, and over time can cut through your seams (source: The Art of Classic Quiltmaking by Sharyn Craig and Harriet Hargrave).
A lot of my quilting buddies use Mettler and have no issues with it, although it is no longer 3-ply.
Hope you find something that works for you.