When doing point-to-point wiring, one is constantly flipping from one side of the board to the other - to locate a hole into which a wire will go. There are many ways to kluge a marker for this - but a "dedicated marker" would handy thing you could sell or (almost) give away with each proto board you sell.
A soft plastic piece with one end as a circle - to grasp with thumb-fore finger, and a tapered pin that would easily go into a PCB thru-hole, but as you push further, the taper would help "lock" the marker to the board. And of course - having a variety of colors would be a huge asset as well - for obvious reasons!
I can't tell you how many times I've used snips of wire only to have them fall out as soon as the board is moved. A colored marker pin is not an earth shattering "tool" but one that would help end lots of frustration.