Man I can't wait. Tomorrow I put down the rest of the payment and get the paper rolling on my Walther P99 Military in 9mm. Course, half the giddyness is it's my first firearm, first handgun, and probably a bunch of other firsts.
From what I've read the .40 shoots very well. There WERE issues in 98/99 with the .40 having some problems, but about 99% I'd say were due to Walther having a short run on slides. They got S&W to manufacture about 3-4000 slides for them. I've heard one or two had occasional FTF's, mostly in the < 500 rounds area. There are a few threads on The Firing Line in their Semiauto section that speak in much more detail about them.
My rec would be to avoid the SW99 (and ESPECIALLY any with the slide labeled SW99NJ!!), and stick with the actual Walther P99 and you should be fine. Only thing that bothered me about the .40 is that the hi-caps only hold 12, while the 9mm hi-caps hold 16.
What did it for me was the grip. It was, stock, so damn comfortable it felt the gun was a part of my hand. Plus the adjustable grip works for my big ass hands. I ended up deciding between this and a USP9...the grip and the trigger did it for me.
Plus, there are limited number of threaded barrels out there, so that you can attach a silencer to the P99.