On all my basses, I've used glow-in-the-dark fabric paint. You can pick it up at any Arts & Crafts store for a couple dollars. It comes in dozens of colors and several glow-in-the-dark ones as well.
Scribbles and Polymark are the ones I use:
It comes in a squeeze bottle and you can have it just come out a drop at a time. I put a small dot on each side marker. It dries cleanly and works perfectly - it will show up under stage lights, or if you have a light show going on, the glow feature really helps on dark stages.
If you want to take it off, you simply peel each dot off. The paint takes on a rubber-like consistency and doesn't leave any permanent mark or residue on your bass.
Kind of a poor man's LED's
