Fresher’s Dilemma: .NET vs Java/J2EE
I have been asked this question as many number of times as the world population. And of course, some people have asked it more than once. My answer is simple: “Doesn’t Matter”. You will get (or not get) a job either way.
Let me clarify that a company basically does not look for a Java programmar or a .NET programmer. First of all you need to be a programmar. That is where most of the freshers lack in the current world. If your computer science fundamentals are strong and aptitude is good, picking up either of these is a two months job. I have reiterated this in many seminars/articles/talks.
Assuming you have strong fundamentals, which one you would prefer to take as a programming language of your choice?
As of now, there are more jobs in Java than in .NET but incidentally the competition is a lot less in .NET 
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Choose one…any one. And stick to it for quite some time. Does not matter if you are not able to attend walkins/tests in the other stream. There will always be good number of jobs in your own stream. And remember, strong fundamentals would always be preferred over syntactical knowledge of either language.