I got a non-scratch adhesive pad with my mag mount - I think it works pretty well, but there are a few scratches on my roof that I don't remember from before (but I think they're from times that I forgot about the antenna before going into a garage - whoops).

At work, we've got a special pad to put under our mag-mount amber roof light.  It's a thin version of that rubber mesh drawer liner material. I think you'll find it in the housewares section of Canadian Tire.  It's non-slip, so it holds pretty well.  Just remember that thinner is better for the magnet to do its thing.

My van has a built-in roof rack, so I just wrap the cable around that to stop it from flapping around.  And I feed the cable through one of the rear windows so it doesn't get in the way of any of the doors.  I guess those are "van-specific" solutions, though.

Jeff