Yeah depending on your app, likely the nV is the way to go.
The mod is a softmod so it's easy to enable/disable.
At the heart of them the cores of the Geforce and Quadros are the same, and actually often the gaming cards are clocked a little faster. Two of the main differences, other than the drivers of course, are yes the certification process which is supposed to guarantee a quality board with reliable parts, and most of the Quadros come with Dual DVI.
I would suggest giving your application a try with just the regular gaming board, then SoftQuadro or SoftGLing it, and then see if you notice improvements in your application. If it's for OGL gaming, maybe forget the Quadro part all together. But for apps you should see a benifit from the moded drivers.
I posted a review a month or two ago that showed the difference, and the FX5900 achieved like 8 out of 9 (IIRC) increased results from the moded drivers. And appreciable increases not just a 1-2% gain.
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