For piecing, my favorite thread is Aurifil 50wt 2-ply. Sometimes I use an inexpensive 60wt polyester thread in the bobbin:
http://www.amazon.com/Spool-Embroide...dp/B00BLWDWT2/ The reason for using fine thread for machine piecing is because it's easier to get accurate 1/4" seams.
I no longer hand applique. A lot of people like 100wt silk thread for applique or the SuperBob thread collections:
http://www.superiorthreads.com/shop/...er-bobs-donut/