One or the other! Does your board support SLI buy the GTX, does it support CF get the HD, does it support both or neither toss a coin!
In all reality just look at benchmarks for the games you play @ your resolution and decide from that. http://www.techpowerup.com/reviews/HIS/Radeon_HD_6850/2...
They are basically equal in performance. You need to decide which is better for you on your own. The main differences will be in feature set;
Nvidia: Cuda, Physx, slightly superior DX11 performance
AMD: Eyefinity, MLAA
I have the MSI GTX 460 1GB and I am VERY impressed with the power it comes with (Came from a 9600GT ). I believe that the 460 has greater OC headroom, but im not 100%. And i do believe that the 6850 starts out faster in most games, but more OC headroom on the 460 could change that... There was a toms about the EVGA GTX 460 FTW (A GTX 460 which is super factory OC'ed to 850 Core... I would get a cheaper 460 and manually OC) and how it overtook and tied the GTX 470 (More power than the ATI 5850) in most cases.
But you need to consider what games you want to do. As jyjjy pointed out Nvidia has Cuda, Physx, and better Tesselation (DX11), but ATI has Eyefinity (You can use three monitors) and MLAA. Also as rolli59 said, you need to decide what your motherboard allows, and look at the benchmarks for the games you play and plan on playing.