Linux RAID4/5 will probably be faster, however the NIC drivers might be slightly slower or not support jumbo frames ;-) just my experience.
Be aware that an AthlonXP or Duron, especially if underclocked/undervolted will probably run faster and just as quiet as a VIA if done properly. SilentPCreview.com has a thread of motherboards which let you do this... haven't checked it in a while though. However stock speeds on a slower AthlonXP and a good cooler can certainly be silent as well with the right cooler.
I would suggest you try Windows first and run some tests, then switchover to linux and see what you get. Your main concerns should be network speed and array write speed. It sounds like you are expecting to use PCI gbit cards, which run cheap ($15-$20), but will probably only give a final result of 20-30MB/sec. If you went with CSA or PCI-E gbit you might be able to get another 10-20MB/sec out of the server. Which is another reason to consider an AthlonXP.