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I found this tool http://sab39.netreach.com/Software/Japitools/JDK-Results/46/ which checks for backwards compatibility between different versions of APIs for Java using javadoc.

Is there an tool equivalent to this one for c#/.net?

Here is an example of a comparison between JDK 1.5 and JDK 6 APIs using this tool: http://www.kaffe.org/~stuart/japi/htmlout/h-jdk15-jdk6

+1  A: 

I haven't tried the Java tool you linked to, but NDepend has some powerful tools for comparing two sets of binaries and highlighting any differences.

Tim Robinson