I don't ever use cotton thread for garment construction. It just isn't strong enough for the stress put on it from dressing and laundering. I sew garments (and most home dec) with 100% polyester thread.
I use 100% cotton for piecing, applique & quilting, depending on the size of the thread. If it's a 50wt/3-ply, I use it for piecing & quilting. If it's a 50wt/2-ply, I'll also use it for needle turn applique. Anything thicker than that I would only use for blanket stitching applique or quilting because it will show up too much. The only time cotton isn't really ideal for quilting is if you are working on a long arm. The speed of the machine almost requires a synthetic thread.