Some good car wax that is a milky/pasty white colour that is advertised as "self cleaning" or "removes paint oxidation as you wax" will do a good job on the black marks unless they are really thick. If so then some more aggresive rubbing compound as noted by dabac above is the solution.
Some clear rocker panel stone chip protective film from the same auto parts store can be cut and stuck on to avoid such scuffing in the future. Or if you're talking about the rubber donuts that go onto the exposed part of the brake or shifter cables then toss them and use long lengths of heat shrink tubing that is the right size to slip on over the cables. Just don't shrink the tubing since you want to be able to take it off and use them again when you change the cables at some point.
Permanent felt marker ink is easily removed with some rubbing alchohal. Gasoline may also do the trick. However do NOT use anything stronger such as lacquer thinner or acetone. Those two in particular will most definetly affect your paint by eating into it and making that spot go dull.