I started out using silk thread for hand applique, and it is wonderful, but it's expensive, hard to find in small quantities, and I sometimes had a hard time finding a color that would work. So I started using Bottom Line and it is awesome. It sinks into the fabric as well as silk, is available prewound on bobbins (so I'm not buying hundreds of yards for a foot's worth of applique) and if you get one of those assorted-color donut packages, you pretty much get any color of thread you'll ever need.
