The AF-S version has more precise AF, and better sharpness at wide apertures at long distances (where the 60mm AF-D is good stopped down but not wide open IME). The AF-S version is well corrected for CA, and better bokeh as well. It is one of my favorite lenses, and has very good price-performance as well as being a great lens in absolute terms. I love to use it for documentary photos of people, as a travel "normal" lens and for nature details as well as technical close-ups. A truly general purpose lens with excellent image quality.
As the others have pointed out the working distance at 1:1 is very short, so I rarely use it for such tight close-ups even though the performance at 1:1 is good. By removing the hood, it is possible to use it at 1:1 and get some light to the subject but I typically use the 200mm AF D Micro for 1:1 work in nature, to get more working distance. For subjects requiring less magnification I really like the 60 AF-S.