This paper "Performance Report: Multiprotocol Performance Test of VMware® ESX 3.5 on NetApp Storage Systems" by NetApp and Vmware was written in 2008 is a interesting comparison with 3 protocols, FC, iSCSI and NFS. The variation between the protocols is about maximum 9%. With the advent of the new Vmmare VSphere, 10G with TOE etc, the performance gap may be close that in 2008.
The summary of the pro and cons as mentioned in the article is summarised at Multiprotocol Performance Test of VMware EX 3.5 on NetApp Storage Systems
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