This is one of those classic "it depends" answers based on the setup. Are you compiling the applications with .NET 2.0 in Visual Studio 2008 or are you targeting a newer framework? Do the DLLs get stored in a shared location (ie., the GAC -- Global Assembly Cache) or are they stored in the application folder?
.NET 3.5 is backwards compatible with .NET 2.0 so you can easily reference 2.0 dlls to a 3.0 or 3.5 application but the reverse is not true.
If you are storing shared DLLs in the GAC you might have conflicts but just make sure the 2.0 and 3.5 versions of the DLLs have a different version and then you will avoid said conflicts.