I concur with using TT with CGI::Application and with other folks who pointed out that TT is useful beyond HTML (for stuff like export files). If you're only gonna learn on template engine, TT should probably be the one.

I've hacked together my own mini application server based on TT, CGI::Application, DBI, and some home brew authentication stuff. With this sitting on the shelf, cranking out new applications is very straightforward.