My friend had a Nikon Mount Zoom I had given her, 28-200 or so, and it had some condensation so she took off the UV filter and the camera "fell" on a rock, putting at least a one inch or more very deep gouge in the outer element.
I took the lens in for repair, and before we sent it in, we shot a roll of film, various openings, in to the sun, in to reflections, and were totally surprised at the lack of any sign in the images. Still had the lens repaired.
I have also heard if you get a "ding" in the outer element it can be filled with black ink.
Finally, the lenses with bubbles in the glass, generally considered to be of good quality.
I do not recommend mistreatment of lenses, but am inclined to agree with what Al says re: the rub mark, it is ugly, and knocks down value, but my old boss at the shop said "a lot of photos have been take through a lens with a scratch".
I have a FSU 85 F2 with a rub mark of some sort in the coating, so it is a user, I just shot with it last week and can find no evidence of image degradation, hardly a scientific test.
I do not clean lenses in the field if I can avoid it, seen too many with "cleaning" marks, I have heard the ones on the back have a greater affect on image? The old soft coatings were famously delicate, and I used to stop in to the shop to get any serious cleaning done.
Same with filters, tests I have seen, seem to indicate it has to be a pretty poor filter to negatively affect image quality.
Just stuff I have seen and heard. It is more painful to look at the damage you have done yourself, rather than a slight mark on a user lens you got at a terrific price.
Almost any Leica body with scuff marks from the meter, or a slight impression or ding, or marks from the straps drops a lot in value, but if you get it cheap, you get an excellent user you do not have to worry about keeping in the case or on a shelf. I picked up a spare M3 single stroke I am figuring out what to do with, and it has a tiny bit of vulcanite missing as well as the scuffs from the meter, so it may get left in the car trunk in a beat up case and a lens with a rub mark. I may look for some "experienced" glass and always have something to shoot with when something comes up on a day I am not expecting it.
Regards, John