For machine piecing my preference is Star cotton thread or the line that Connecting Threads has - I think it's called Essentials. For hand applique I prefer YLI silk although I do have some Kinkame and in a pinch will use any cotton thread. For machine applique I have no preference - color matching is the key for me. I do very little quilting so I let my LA make that selection, what little I do I use cotton.