I'm a CUDA developer with very littel experience with FPGA:s, however I've been trying to find comparisons between the two.
What I've concluded so far:
The GPU has by far higher ( accessible ) peak performance
It has a more favorable FLOP/watt ratio.
It is cheaper
It is developing faster (quite soon you will literally have a "real" TFLOP available).
It is easier to program ( read article on this not personal opinion)
Note that I'm saying real/accessible to distinguish from the numbers you will see in a GPGPU commercial.
BUT the gpu is not more favorable when you need to do random accesses to data. This will hopefully change with the new Nvidia Fermi architecture which has an optional l1/l2 cache.
my 2 cents
