Nvidia boards get a little bit of a gaming boost when used with NV gfx cards. Some people feel that the NF3 is a better chipset especially for OCing, but I believe the jury is out on that one. One thing that seems to be consensus is that the AGP lock on the VIA boards can be finicky or outright fails at some point. My anecdotal experience is that this is less common on NF3.
As far as performance goes, they're very similar due to the memory controller being on the CPU. This used to account for most of the difference in motherboard performance and now it's all equal.
If you ask me, I'd pick mostly based on features and price, but that's just my opinion.
You may want to wait until NF4 comes out, I know a lot of people are waiting for it and then going to PCI-E and/or SLI. That's your choice as well.
The 939 selection is limited, and I am not sure why.