Do you work with Sun Solaris or one of the bsd's such as FreeBSD? If so then you will want to have the VIA chipset in your motherboard since VIA chipsets work with Solaris and FreeBSD while the NVidia chipset does not. NVidia does not currently have plans to produce a Unix driver for its NForce chipset, with the exception of a driver for linux.
I am not sure if it is possible to change the motherboard without reinstalling the operating system. I would presume the system will have to be reinstalled since drivers, memory range allocations, and hardware settings will change. To me it seems to be a necessity to reinsall the OS when replacing the motherboard and processor.
Here is a recent
New Computer thread that received a lot of attention. browse through the General Hardware category for more threads concerning system recommendations. It is impossible to respond to every request for a system recommendation and you will pick up more information along the way.
EDIT: Also go into the Motherboard category and perform a search for "via". There are about 13 threads there, which can be helpful.