I use felt markers, with permanent ink.
Every time I reload a case, it gets a black line from the primer to the rim.
If I want to put more than one specific load into a box, I color only the primers with different colored markers. The permanent type is best for obvious reasons. Helps to keep a log as well.
One buddy of mine, only marks the primers to keep track of how many times the case has been reloaded. Refuses to mix loads in a box. Not a bad habit at all.
I saw a bunch of black cases an bullets at a gunshow recently. I asked if they were milsurp.
The fellow laughed and told me his story. He wanted a bunch of black cartridges for some display he was putting on and soaked a lubricating pad with BINGO ink. They looked OK, just different.
Of course, any colorant you use on the brass will be removed with consequent lube and resizing.