You don't choose one over the other!

A mod_perl application can still use CGI.pm - I do it all the time. I write what are essentially CGI applications but I run them under mod_perl for the performance advantage. I can - however, run the same app in a non mod_perl environment quite easily.

If you write a mod_perl handler based application then it can only run under mod_perl. It is purely a case of how you wish to utilise mod_perl.

jdtoronto