First of all this is not about that kind of religious war.
Often the religious wars between .NET and Java get lost in unimportant details of language and runtime performance. The fact is that often good criteria such as software quality, productivity, maintainability, development support, community support, diversity of frameworks, ease of use, integration, etc are kind of left out. I tried to summarize my comparison in a chart (click on the image below to see it in its original size)
I tried to compare mostly Orcas beta 1 (.NET 3.5) with Eclipse and a bit of NetBeans 5.5.