I have not had a problem with pencil lead rubbing off completely but it will fade a bit. I've used a soft leaded pencil and rub a line mabe a 1/8" thick alll the way around it, short way around for one nest and long way around for another if I want to mark two different clutches. Sharpies and magic markers also can work. You can write the date on with a sharpie but I think writing a date with a pencil may be too light. Depends on the writing and how soft the lead is. Haven't tried that so I don't know for sure. Your goal is to know at a glance which eggs belong to that specific broody.
I try to not go too wild with the marking since the developing chick needs to breathe and I don't want to clog up the pores in the egg shell any more than necessary. For that reason I would not use a crayon or anything waxy, tape, or sticky. A chick might have problems pipping or zipping if it runs into tape or a sticky. I'm not sure if food coloring would clog up the pores.
Don't obsess too much on the marking. I remember as a kid covering a lot of the shell with pencil markings and the eggs hatching fine. I also used fountain pen ink (it was that long ago that we actually used fountain pens) and that worked fine.