Yay Warren - congratulations
Yep - in this class of tower system , RARELY is it Apple-built hardware that ever fails - it's always some 3rd party device such as that video card of yours. I have a bunch of G5's and even more G4 towers at work that I've simply run out of uses for. They don't ever die, they just fade away until I replace them with the latest. My company is essentially an advertising firm and a software development function for the support of said advertising production, so ultra-reliable high-end gear is of critical importance. Our customers don't like missing publishing deadlines and I simply wouldn't risk our business on anything less. Using Apple graphics workstations has been a very solid decision so far for us (10 years).
As far as the 3D desktop goes, I don't know. From the patent outline it looks and sounds impressive, but whether it's a leap forward or sideways only using it will tell. I guess that you could potentially fit more work in progress on a desktop because it can be stacked obliquely, and if that were the case then it would likely suit some users better than others depending on their workflow. I'd have to see it in action, but it looks like it's kind of cool. I don't want to sound like a broken record here, but I trust Apples innate sense of engineering on these matters. It's not often they introduce "bling" - unless it works. They have always had a design sensibility that produces a clean, easy to use and aesthetically pleasing place to be. I can't imagine that they'd bother developing and patenting a 3D environment for the hell of it.