Depends on the kind of stencil. If it's the mesh kind where the lines you mark are covered in mesh, you're supposed to use chalk/pounce, in which case I just use the pounce since I have one. I have the blue chalk, not the iron off kind, but I've had some issue with removing the lines in the wash so just be careful.
If it's the kind where the lines are open, I much prefer to use Crayola Ultra Washable Markers. I always wash my quilts in hot water, then warm water after they are complete, and have never had a problem with any of the colors washing out. I've ironed on them, left them on for many months (a year?), and they've always washed out. So great. It's obviously more work than a pounce, but the lines are easy to see and come in a variety of colors, plus cheap.