Oh man, where to start.
First off, both the P99 and SW99 are amazingly accurate, egonomic, easy to shoot fast, and easy to care for.
The P99 has a tennifer treated carbon steel slide like Glocks, whereas the SW99 has a melonite (basically the same as tennifer, slightly different waste chemicals left over from the process) treated stainless steel slide. Both are pretty much imperveous to rust unless you take them swimming.
In 9mm, both are available with 16 round mags. I've read on the net that some people have reliability problems when loading the mags to 16rnds, but I have over 25k rounds through my gun and none of my 6 16 round mags (or my 2 10 rounders) have ever had a problem.
Both are available in a variety of trigger configurations.
P99-AS trigger- DA/SA trigger type with third AS (long SA pull) available if you like it. Most people I know carry them decocked and don't really use the AS option. The SW99 is identical.
P99-QA trigger- Glock like trigger that leaves the striker partially cocked and offers a consistent trigger pull. It's about a 7-8lb pull that is shorter than the stock glock trigger pull. The SW99-OL is the S&W equivalent here. Not as popular as the AS trigger style, but still a sweet shooter.
Both guns are available in DAO, but honestly, why?
Quality on the Walther is top notch. At least as good as HK's polymer offerings, better IMO. I've not actually fired the SW99 before, but they seemed well built handling them. I've studied drawings of the two side by side and they are pretty much identical aside from the exterior cosmetics. I can't imagine the SW99 being inferior in any way based on those drawings. If the assembly quality is the same, and the internal components are the same, the SW99 should be every bit as amazing as the Walther. Shipwreck can offer more insight on the side by side comparison though.
S&W is discontinuing the SW99 now that they have released the M&P series. Walther is making all trigger styles still, but Walthers always make it to the US in smaller quantities than other manufactureres so you may have to look hard in some areas for your preferred trigger style.
Takedown of both can be done blindfolded in about 2 seconds. Putting them back together takes about 5 or 6 seconds. The gun breaks down just like a Glock, but you don't have to pull the trigger to get the slide off. Field stripping takes the gun down to 4 components: slide, frame, barrel, and recoil rod/spring. The gun likes to be run with minimal oil just like a Glock.
I can't say enough good things about this gun, but I'm sure a couple of dozen others will be along shortly to make up for my lack of praise in this post.
P99 is simply the finest combat handgun available today. I love it for CCW, and if I could use hollowpoints, I'd take it over anything else in a combat enviornment.