I went for the 60mm for two reasons. One is that I wanted something to replace my "nifty fifty," and the other is that I already had a 100mm f/2 as my portrait lens. If you need greater working distance (e.g. for shooting bugs), then you might prefer the 100mm f/2.8. The 100mm will also be better for portraits since it gives you greater background magnification. However, the 100mm is a long lens, so it's not much good for shooting in small spaces. Also, if you aren't using a tripod, the longer focal length will mean more camera shake.
I really like the working distance of the 60mm lens, but I don't ever point it at insects (I'm too squeamish!).