Actually, looking at the new nvidia cards, it may no longer be a problem.

When I put together the shuttle games machine, the high-end nvidia card was the FX5800, which had a soddin' ENORMOUS fan and heatsink on it, which used up an entire extra slot to the left of the card. The shuttle motherboards have (unusually) the AGP slot to the left of the PCI one, so if you attempted to fit an FX5800 card you'd find that the fan assembly stuck out past the side of the case by about a centimeter. I ended up going for a 9700 instead, which aside from anything else was faster anyway, and fitted neatly.

Now, however, it seems that the FX5900 chipset has a better thermal management system(tm), as can be seen here. You may well find that everything fits, although I'm not sure whether the power requirements might be a bit much. That said, the 9700 isn't exactly low-power either, and it's fine in my shuttle.

pca