I own a 2000 996. That car has been my daily driver since the day I bought it in mid '06. It currently has 110,000+ miles on it, of which 73,000 miles have been with me. It's also been used about six times on the very high speed Willow Springs raceway, beaten to within an inch of its life every time, and has been autocrossed as well. Other than a voltage regulator that failed about four years ago, it has been absolutely reliable.
The biggest potential issue with these cars is the possible failure of the IMS bearing. However, Flat Six Innovations has a redesigned bearing that is much more robust and which addresses the core problem of the bearing. It's an easy retrofit during a clutch change and essentially eliminates the potential of an IMS bearing failure. One of the recommendations for IMS bearing health is to change the engine oil frequently, maybe every three to five thousand miles (which is what I've always done, btw), which the experts feel seems to help keep the bearings healthy. The D-chunking issue seems to have been addressed by Porsche as well, and doesn't seem to be a common issue anymore.
The engines themselves, assuming the IMS bearing has been replaced, and the optional deep sump, baffled oil pan has been installed, are said to be quite robust and survive track work in the spec 996 and Boxster series quite well. As I said earlier, I've beaten the heck out of my bone stock 996 (with a stock and original IMS bearing and normal oil pan) out on the very high speed Willow Springs track and the car has never shown any issues whatsoever.
As far as handling is concerned, in bone stock US spec form, it's very good and forgiving, but could certainly be tightened up a bit. Fortunately, there are plenty of options out there. One is the R.O.W. M030 sport suspension setup, complete with struts, springs, and roll bars. It completely changes the handling character of the car and gives it a much better, lower stance. Taking it a bit further, you can opt for the X74 suspension, which gives the car near-GT3 handling and stance - although it might be a bit harsh for most. For about the same money, you can also opt to go with a fully adjustable Bilstein PSS10 suspension setup. For more camber adjustment, you can go with GT-3 lower control arms.
I would recommend visiting the very active 996 forum at Rennlist.com. There are quite a few guys there who have well over 100k miles on their 996's.