Whether I quilt on the applique or not depends on the size and composition of the applique. If it is really small, I usually only outline quilt around it. If there are individual pieces in the applique, I quilt around the individual pieces as well as the outline quilting. As has been suggested, veins in leaves often work. I have seen a lot of machine quilting, not custom, with an overall pattern that quilts right over the applique. I prefer custom quilting to highlight the applique, but it depends on the quilt, its purpose and the intricacy of the applique