It depends on what you want.
-nVidia strengths:
-Quality Linux drivers
-Quad-SLI
-SLI maturity
-Strong OpenGL support
ATi strengths
-Impressive hardware
-Fastest single GPU on the market
-Strong D3D support
ATi's weakness is Crossfire's maturity. It was released much later than SLI and the driver development shows. It's much better than it used to be, but SLI still is a little more polished. In general, ATi's achilles heel has been drivers, but overall, they're much more on par with nVidia these days. ATi has consistantly had hardware that is simply better than nVidia's, but they've short changed it with bad drivers. Lastly, ATi's Linux drivers are...well...crap.
nVidia tends to rely on more brute strength, and their GPU's are as optimized on the silicon as ATi has.