From your example, if I write a Forum::Format module, then all my code dealing with it looks like: my $ff=new Forum::Format;. If someone doesn't like part of it and wants to inherit and over ride that sub, say his new module is Forum::Format::NoHtml how does he tell my application that it should be using this New and Improved class/object instead of the regular old Forum::Format

Don't hard code the class name. Have a factory that gives you the appropriate formatter object based on a configuration file, environment variable, mod_perl setting or whatever.

Take a look at Class::Factory for one way of doing this.