At my company about a year ago, we held a Java vs .NET seminar. The attendees were probably 10% .NET, 80% Java and 10% interested onlookers (like me). The main .NET guy stood up to speak. He said he'd done this project recently in Java and that project in C# and these were his experiences. He talked about the maturity of the tools, particularly VS vs Eclipse support for programming in the large, LINQ, he mentioned that in the Java world there were many competing frameworks whereas a C# developer could get up to speed on a project without having to learn a new one, a whole bunch of stuff. He was calm, articulate, prepared, and clearly had the attitude of "the right tool for the job" and "what's best for the company".

Then it was Java's turn. Their speaker hadn't prepared any examples, and he'd never used .NET. I scented blood in the water. This was going to be fun. It went something like this:

Him: Java is cross platform! Me: So what? We only use one platform for all Java, the Ops guys insist on it. Him: Java is used by lots of large companies including X, Y and Z Me: All of whom write their major products in C and C++ Him: You can use lots of languages on the JVM! Me: So the best thing about Java is that you don't have to use it? Is that all you got?

Then he prepared his killer blow:

Him: Java is not Microsoft! Me: Haha, OK you got me there. No wait, there's Mono...

IMHO right now Java should be considered a legacy language, and Java programmers either assigned to maintenance or those who are good, retrained (not necessarily in C#, there's Scala for example). The JVMs are generally good and if you need a VM language on Unix then worth considering (tho' there are other VMs out there). Personally, I would advise against starting a new project in Java.