Recently The Middleware Company releases a report based on a study which Microsoft sponsored to compare .NET against IBM WebSphere in a number of dimensions including developer productivity, manageability, reliability and application performance. The report shows not only the results but also shows the steps and processes prior to the conclusion.
You can find the report here.
You can also find what the Java community has to say about this.
My personal opinion is, never to based on any conclusion made by other parties, if they're not based on hard facts and good reasonings, especially if they're too high-level. I haven't got a chance to read through the report, but I hope I can find something to learn there.. :D
Further Reading:
Enterprise Java Programming with IBM WebSphere Second Edition
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