I haven't looked at Merlyn's module yet, but I will.
CGI::Application can be quite painful for making lots of apps do different things, and I didn't like it. I wrote my next app using RubyOnRails because of my experience with CGI::Application. Yes, C::A was a huge improvement over raw CGI when I first found it, but it still made coding un-fun and felt a little raw.
There is NEVER anything wrong with reinventing a wheel when you think it's square, after all, you personally have to use that wheel. I am a *huge* proponent of clean code and good design ... wherever it can be found. Honestly though, I doubt I'm leaving rails anytime soon.