I have owned an XD .40 and a Walther P99 .40 AS.I happen to go through guns like white T shirts...I just sold the P99 .40 AS to a local place and got $425 for it.
I personally like the XD platform much more as a whole. Don't get me wrong, the P99 AS is a VERY high quality sleeper that doesn't get the credit it deserves. Has great ergos, a nice single action trigger, I like the decocker, etc. It just wasn't for me. I think the XD trigger is just as good as the P99s since it is basically a permanent single action. I actually like it better because it stacks up just right before it fires. It just has a good, consistent squeeeeeeze, POP....still light and crisp though. I don't like safeties at all, but the XDs have 2 GREAT natural safties built in. It adds piece of mind, and doesn't get in the way because you don't have to worry about whether or not the gun is in DA or SA mode or whether or not the safety is on or off. Super safe, but always ready to go when you grab it and pull the trigger...and no surprises. Same trigger pull every time and it also has a more comfortable shape than the P99 IMO. I also like the loaded chamber indicator and cocked firing pin indicator on the XD. The bore axis is lower on the P99, but the XD absorbs recoil better and feels better when shooting overall.
I have normal sized hands and fingers, and for some reason the P99 starts to hurt my trigger finger after a few magazines. The mag release is actually pretty convenient and I like it. XD also has good ambi mag release though. There aren't too many sight options available for the P99 either. I don't like the rear detent system that holds the sight in place, and I don't like the pinned in Glock-style front sight either. I think its plastic too...
Also, the P99 isn't too light friendly. There isn't as much room up front like there is with the XD. My TLR-2 light/laser was a far better fit on my XD than the P99. I had to take out the little knobby thing on my TLR-2 that goes into the notch on the light rail for it to even work with the P99. This is less secure since the light would just slide right off if it loosened up after lots of shooting. I'm not too sure how the Surefire lights work with the P99. It also just looked better on the XD.
Last but not least, I just didn't like the "feeling" I got when holding/shooting my P99. It just doesn't feel as solid and "badass" enough for me. The whole look and feel is just a little too elegant for my taste. I like the blocky, mean look of the XD vs. the sleeker, wimpier look of the P99.
It's really up to you, but I have to tell you that you will NOT be disappointed with either gun. I'd save the money and go with the XD if I were you. If you are like me, you will end up happier in the long run with it. Just my 2 cents i guess....good luck.
*edit* I will also agree with the guy above that accuracy with my XD was much better than the P99. The P99 was praised for its accuracy, but I didn't get this experience. I still shoot the XD more accurately than any other gun I've owned. Everyone is different though and it was obviously just me that couldn't shoot the P99 accurately.