This is a short test that will ensure that controller dependencies are bound appropriately for Ninject. For this to work, you either have to make the bootstrapper public or mark it internal and add the InternalsVisibleTo attribute to the assembly.

gistfile1.cs

[Test]
public void ensure_controller_dependencies_are_bound()
{
    var assemblyName = "MvcApplication4";
    var assembly = Assembly.Load(assemblyName);

    var parameters = (from type in assembly.GetTypes().Where(
        t => t.IsAbstract == false && typeof (Controller).IsAssignableFrom(t))
                        from constructor in type.GetConstructors()
                        from parameter in constructor.GetParameters()
                        select parameter).ToList();

    NinjectWebCommon.Start();

    foreach (var bindings in parameters.Select(
        parameter => NinjectWebCommon.bootstrapper.Kernel.GetBindings(parameter.ParameterType)))
    {
        Assert.IsTrue(bindings.Count().Equals(1));
    }
}