Many orgnizations are currently considering and evaluating .NET and Java (J2EE) as their enterprise application development platform.
I found a very good site which contains extensive materials designed to help you evaluate Microsoft .NET vs. J2EE application server technologies. It contains downloadable whitepapers, benchmark comparisons, and sample source code.
Evaluating .NET vs. J2EE
Well I am sold on .NET for a long time now. I hope the link above helps to make your decision easier.