I sometimes use paint pens like the ones JD mentions, but they tend not to be very matte so I don't use them where a reflection might cause problems. Likewise sharpies have a purplish sheen, and they can wipe off metal surfaces easily as mentioned.
For camera interiors and sometimes lens baffles I use the mattest enamel paint I can find, the brand depends on where you are in the world. Chalkboard paint can be OK, or pot belly black. Mixing calcium carbonate powder in can make paint more chalky and matte, also adding fine sand gives a texture that helps disperse light reflections. Telescope shops sometimes sell ultra matte black touch-up paint for telescope interiors.
For a really non-reflective surface needed on things like long lens barrel interiors I use sticky-backed felt.