Originally posted by Digitalis as far as I know the only difference between the two lenses is the number of aperture blades (8 Vs 9 - a trivial difference numerically, but it makes a big change in how OOF highlights are rendered ) and some updated lens coatings apart from that; they are optically identical.
You've got your info a bit off, there. Bother versions of the D FA 100 mm Macro have 8 aperture blades. However, the blades on the WR version are shaped in such aa way that they make a nearly perfect circle at wide to moderate apertures. So if you're shooting at, say, f/5.6, you have the benefit of a circular aperture, instead of a rounded octagon like the lens might normally have. This will affect out of focus rendering, but given that macro shots are usually taken at much smaller apertures, it may not be a big deal. Should affect portraits, however.
The other big difference between the old and new 100s is the construction. The WR lens has a metal body and feels quite solid. It is on par with the DA Limiteds in build quality, and shares the same general external design. If you're a sucker for well-built hardware, the WR is hard to pass up.