For me, it depends on the look I want and how I will quilt it. Polyester is puffier and I like it for hand quilting and occasionally for machine quilting. Polyester tends to be a little slipperier when machine quilting for me but still manageable if I use 505 basting spray.
I like 80/20 cotton/poly batt for machine quilting better but it tends to make hand quilting difficult. I have not tried wool, silk or bamboo but many like those but they are a bit more expensive generally.