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It seems the nvidia one has better driver and developer support, however I have seen reports that their shader compilers are a bit on the benevolent side. They do accept things not strictly standard which later makes trouble for ATI cards. On the other side, I still remember fglrx problems I had.
Btw, imo this is only a problem if you want to do software development, doesn't matter for an end user if stuff that's not supposed to work does. If you go for software development on an nVidia card (and drivers), remember to have the project tested by users who have some other card and/or drivers.