On the one hand NVidia has MUCH better linux support but the ATI is overall faster and has better image quality.
ATI also actually releases info to the DRI Project et. al. so that you don't necessarily have to depend on them for drivers. In practice however NVidia's Linux drivers seem to be much better, since they're basically the Windows drivers wrapped around a Linux interface (or so I'm told; would explain also why they made up a replacement for DRI). AFAICT, ATI's Linux drivers are (were?) kind of a side thing from the FireGL guys to support workstation clients.