Way back on my NVQ course we were told to use permanent markers on glass, and I've never really thought much about it, coping with dark glass as best I could and then forgetting about the problems with it until faced with another piece of dark glass on the bench that has to be cut to shape. I've generally used a black 'Sharpie' pen to mark up glass, which are easily obtainable and leave a permanent line, but I've found it very difficult to see the line on some darker coloured glass.
I took an offcut of Wissmach Midnight Blue English Muffle into our local stationers - Howells of Biggleswade - earlier this week, and tried a couple of pens.
I found that ballpoint gel pens (available in gold, silver or white) work quite well - certainly clearly enough to see the line to cut, and the line left by the gold pen is narrower (perhaps 0.2mm) than that left by a slightly worn Sharpie (which could be upwards of 0.5mm). The gold line may not be quite so permanent as that left by a Sharpie but it's more than adequate for the temporary marking needed to cut a single piece.
The gold line stands out much better than the black on red water glass (the black line can just be seen, to the left of the gold one):
I think the gold gel pen cost £1.49 so didn't break the bank, and the shelf over my workbench now has one ready for when I need to mark some dark glass.