If your application requires portability on different platform, Java has more options than .NET.
2. Requirement of extent of Scalability
Java starts with scalability while .NET starts with simplicity, if you can handle the complexity you can enjoy the scalability of Java. Otherwise you can be stuck in between.
3. Size and budget of the solutions
You also have to consider the size and budget of your solution, If you are developing a small application neither of these suits you enough--ignoring all other factors--you may have other cheap alternatives like InfoPath, MS Access, Excel Applications
4. Complexity of application (processes, transactions, interfaces, integration etc.)
Business applications comprise of complex in-memory transactions are better to be built on Java, thanks to application servers. .Net is still lacking mature and reliable in memory transacion handling. Database driven applications not having complex business processes usually cost less on .Net.
5. Availability of development skills and infrastructure.
If you don't have experienced and knowledgeable resources, Java can become a may become a hard nut for you.
6. Integration with Legacy systems.
Usually a vendor's approach is to sick with it's own products, or to prioritize at least. Though Microsoft provides integration with it's own legacy systems but to motivate people to move on earlier product, they often disclaim to support for a long time. Being managed by people, Java gets more marks in this regard.
7. License cost vs. Development cost.
Usually Java brings with more free and open source options as well as more development and integration cost. While .NET brings with easy development and integration with less free and open source options. So prepare for greater development cost in Java and greater license cost in .NET.
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