The only major areas of problems I discovered 2.0-> 3.5 were found in Web.Config and centered around links to System.Web.Extensions 2.0. If you use the Visual Studio interface to change the version of your .NET project, VS will automatically fix most of the reference incompatibilities in your Web.config file.
As for the differences in the code, you will probably find that some methods that were deprecated with newer versions, but I never came across any direct violation.
Microsoft has a very strict backward compatibility compatibility standard so that they can minimize the impact of major updates.
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