CGI::Application is really more of a development framework and philosophy, as I imagine Template::Toolkit is.
I really like CGI::Application and use it for nearly all my web projects. I find it provides useful functions without imposing too much structure on me. It also has a very strong benefit of helping to create highly re-usable code, by maximizing the amount that is in modules. In this structure, it's easy to re-use an application with a completely different template set providing a new look and feel, but using the same core Perl modules.