How to mark a class as Deprecated?

You need to use the [Obsolete] attribute.

Example:

[Obsolete("Not used any more", true)]
public class MyDeprecatedClass
{
    //...
}

The parameters are optional. The first parameter is for providing the reason it's obsolete, and the last one is to throw an error at compile time instead of a warning.

The reason to not erase a class and deprecate instead is to adhere to some "politeness policies" when your code is an estabished API and then is consumed by third parties.

If you deprecate instead of erase, you give consumers a life cycle policy (e.g., maintenance and existence of the classes until version X.X) in order to allow them to plan a proper migration to your new API.

If you are using version control I would recommend just deleting the class. There is no reason to have unused code around.

Version control will be a handy undo if you decide later that you want the class.