One is with a standard server operating as a file server and the other is a NAS device with the Windows Storage Server (WSS) software installed on it. The WSS based NAS device is the better choice for administration, reliability and potentially better performance. Performance depends on what you're doing, so you may or may not see a benefit. WSS has an optimized NFS implementation now.
Go with the NAS device -- the reliability and administrative ease and potential performance benefit make it worth it.
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Whether to use a NAS appliance or a homegrown file server?
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