The first question we need to ask - can these two be compared? A 30,000 ft. view of these two will tell you that Java is a programming language (generally speaking) while .Net is a framework. .Net, as you might know, is a platform that supports several languages viz. C#, VB.Net, F# and others. A framework is nothing but a pool of ready-made functionality available at your fingertips when you are writing code using that framework.
Those who are interested in deeper analysis may perform search on the Internet to find out which among the two scores over the other for specific aspects. But generally speaking; both Java and .Net are quite robust and have found applications world-wide in very complex projects.
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