General: Middleware co. study of .NET vs J2EE/Linux
This detailed study, sponsored by Microsoft but with constraints to avoid bias, is about an example Enterprise application implemented in three different projects. One team used .NET, SQL Server, and Windows 2003; one team used IBM WebSphere, Linux and Oracle; another developed for WebSphere using Rational Rapid Developer:
It's a good read, with lots of interesting points about the differences in philosophy between the different platforms, and how this played out in actual development. Although the outcome is favourable to .NET, I've put this under a "general" heading, since in the end it is just one example; change the teams and a few other variables and the result might have come out the other way. I recommend it though because there seem to be very few studies of this kind either performed or published.