I use the EF-S 60/2.8, EF 100/2.8USM, and EF 50/2.5, the latter two on FF as well as 1.6-factor. If you are not looking over your shoulder at moving right away from 1.6-factor to FF, then the 60/2.8 is significantly preferable to the 50/2.5 for its much better handling (including full-time manual focus) and its range to x1, for which the 50/2.5 requires the (quite expensive) Life Size Converter (which does actually work very well) or an EF25 tube. Also, for general use, the 60/2.8 activates high-precision focus, wheras the 50/2.5, despite being a faster lens, has a special flag set in its 'handshake' with the camera that limits it to normal precision. Optically there is little to choose between them. I prefer the 60/2.8 strongly for fieldwork, but (even on 1.6-factor) I find that the 50/2.5 is the better lens for copying artwork.
The 100/2.8 is a much bigger and heavier lens than either the 60/2.8 or 50/2.5. It covers the same range of magnifications as the 60/2.8, to x1, but with longer working distance. It's a great lens on FF, but on 1.6-factor it can be a bit in-between - the working distance is inconvenently long for a lot of medium close-up work, but not long enough for insects like many butterflies and dragonflies. It has the added advantage of a focus-limiter switch, but the disadvantage that, because it uses a 58mm filter, you can't mount a filter and a macro flash together, whereas you can do this with the 50/2.5 and 60/2.8, both of which use a 52mm filter.
My advice would be to go for the 60/2.8 initially. If you then decide you want the 100/2.8, very likely it will be to supplement rather than replace the 60/2.8.