I believe this is a limitation of all the current trunking technologies (at least, the one that Sun, Cisco, NetApp, and 3Com use for 100bT in any case).
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Exactly. Many EtherChannel and EtherChannel-style trunking algorithms use MAC addresses to distribute the data down the pipes of a trunk. Therefore, if you only have 1 client, these implementations will only use one pipe. NetApp simply reflects the response down the same pipe the request came in on. So if you only have 1 client, Gbit is the way to go...nice big pipe. You get no throughput advantadge from a multi-trunk due to these switch algorithms.
Now SUN orginiation with SunTrunking *does* have a mode which provides round-robin rather than mac-hash link selection. I had a 740 with multiple links to a backup machine with a qfe card. With round-robin set on the sun, we got very nice link utilization.
Of course this is only useful for direct connections, not when you're travelling through Cisco switches...