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Well, they both go to 1:1 magnification without any additional lenses or extension tubes and they are both f2.8, so they are pretty similar lenses as far as functionality goes.
The 100mm giives you a bit more working distance. It goes to 1:1 at 31cm, while the 60/2.8 goes to 1:1 at 20cm. The 100mm macro covers a full 35mm frame while the EF-S 60/2.8 macro only covers the APS-C frame.
The EF-S 60/2.8 is considerably smaller and lighter and it's also over $100 cheaper.
If it was me, and I wasn't thinking of upgrading to a full frame camera anytime soon, I think I'd go for the EF-S 60/2.8 macro USM, based on size, weight and cost. It's a very sharp lens.
If I was thinking of getting a 5D or other full frame body at some stage (or if I still wanted to shoot film), or if I really needed a little extra shooting distance, but didn't mind the extra size, weight or cost, I'd go for the EF 100/2.8 macro USM.
Another small advantage of the EF-S 60/2.8 macro is that it can double as a portrait lens. A 100mm lens on an APS-C body is a bit long for portrait work unless you stand at quite a distance from your subject.