Ahh the eternal quest of finding a suitable marking tool will never end. I have had great luck with the following:
For dark colors:
I use a Fons and Porter Mechanical pencil with the white lead. However it rubs out very easily so I would not recommend marking the whole top with this. You have to mark as you go. Great for handquilting with a lap hoop and plays nicely with stencils.
I have also had great luck with Transdoodle brand transfer paper. Again rubs out very easily so you can only mark as you go unless the quilt is going in a rack of some sort. In fact the mark is almost like chalk and I usually go over it with the F&P pencil when handquilting. But in a rack it seems to hold up then. It comes in blue, yellow red and white and I have used all colors and had all wash out. Transdoodle is for having a preprinted or predrawn design and you want to transfer on to the quilt top. It is the same basic idea as old fasioned carbon paper or transfer paper used in tole painting.
Pounce pad and stencils works well for me when longarming. I have only used the regular chalk kind not the ultra that you remove the marks with an iron. Both blue and white have come out fine so far.
Light colors:
I have had great luck with another Fons and Porter product, the water soluble graphite pencil. Packaging said to do first wash in plain cold water NO SOAP. Some detergents can permanently set the mark. I have only used this tool to completely mark out a quilt that went in my LA rack so do not know how easy it would rub out when handquilting.
Many moons ago I read somewhere that you can starch your quilt top and then mark with regular pencil. The lead marks "float" on top of the dried starch and when laundered the marks wash out with the starch. I did this once with handquilted quilt. This quilt sat for years before I completed it and I had premarked the whole top. All the marks washed out. I don't know if I was just lucky or this really worked. It certainly seemed logical about the lead sitting on the starch and the starch washing out. Starching also made it a lot easier to lightly mark with a pencil. I used a regular pencil and marked very lightly.
Things that have not washed out for me:
Yellow quilt marking pencils
Blue chaco liner chalk
I have not tried the blue water soluble markers or the disappearing ink markers. Still a little afraid of them but many MQ pros swear by the blue wash outs.