When it comes to Linux support, it's a mixed bag. I always found it easier to install Ati cards rather than Nvidia cards. However, Nvidia lets ya tweak it more so that you can squeeze out that extra performance (all tests done with Debian 2.4).
Workstation, I'd give Nvidia the edge. Highend to Ati. Mid-stream to Ati also. Low end will depend on how much the 5200 Ultra's cost compared to the 9000 pro 128 mb.
Just me $0.02
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