Drivers and compatibility is a major reason not to upgrade. As far as 64 bit OSes go, you might as well just buy everything new - a new MS Office (~$400), new audio and video apps, new cad/cam apps, etc. Since you're building the machine from the ground up, you're already getting new hardware anyway, so it's just a matter of time before the 64 bit drivers come out. You just have to be patient.
Or you could run OSX... But then you're limited to the number of apps. Not that that makes any difference because you're limited by the number of apps. anyway.
We went through this when we changed over from W98SE to NT4.0, W2K and WXP. We end up buying completely new software. Some time in the future, when we go to 128 bit processing, we'll go through it again.