Dare Obasanjo has updated his comparison of Microsoft’s .Net 2.0 C# and Sun’s Java 6.0 programming languages (via Hartmut Wilms). It is a detailed comparison, it includes both concepts and implementations.
It will not be helpful to decide whether you should use C# or Java for your project, something else rules that world. It will be more useful from a learning perspective, especially if you know one of them. The comparisons highlights some of the aspects that you would not notice otherwise, like the design for creating threads or fall-through in switch statement. A good resource for learning.