It seems that in certain server scenario situations, Intel's Hyperthreading technology can actually drastically hinder performance, resulting in a bogged down server with heavy CPU load not getting much done. The problem stems from the fact that two threads would share the same cache when being executed, and certain threads would cause the cache to be filled with something useless. It apparently degrades performance in these environments so much as to have some people suggesting disabling it.

"It's ironic," said Ibbotson. "Intel had sold hyperthreading as something that gave performance gains to heavily threaded software. SQL Server is very thread-intensive, but it suffers. In fact, I've never seen performance improvement on server software with hyperthreading enabled. We recommend customers disable it when running Citrix and our software on the same server.
HT likely fits much better on the desktop, where this type of scenario is seldom seen. It may be of interest to those who use suites like Vmware, however. Intel has not yet responded to the findings.