By accident, I used a wet/damp microfiber towel to wipe off my shoes recently. The fabric really wiped out the black "scuff" marks with out any damage to the shoe. I now wipe off my shoes with a microfiber towel as soon as I get home.
Still, as Tar Heel said, saddle soap is best for leather and does a great job of cleaning a shoe that's been needing a bath for some time. If you have an old pair that's stiff, use liberal amounts of saddle soap and watch the leather recover.