Here’s my initial take :
If you want your project to run in windows only and future versions of it and don’t forsee any major changes in platform,then surely go for .NET,.NET is especially made for windows,since it provides a very good UI,also it is very easy for referencing external assemblies very efficiently for your project,which Java programmers find it very difficult.
Now if your project needs to run on Linux or UNIX as well (or maybe even OpenVMS),then surely go for Java.
Java’s advantage is it is supported in almost all platforms ( even Windows ).
Good analysis. Web Services are far easier in .Net as well. From a company’s cost perspective, .Net programmers can be more efficient, and thus they save money.