There's nothing inherently wrong with having 40 cgis and CGI::Application supports that. Sure, the cgi is quite simplistic:

use strict;
use My::CGI::Application::App;

my $app = My::CGI::Application::App->new();
$app->start_mode( 'run_mode_that_matches_cgi_name' );
$app->run();
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That way you can have distinct namespaces for the modes of your app --- think /cgi-bin/search, /cgi-bin/results, /cgi-bin/display ... that's a bit better (IMHO) than /cgi-bin/app?mode=search, /cgi-bin/app?mode=results, /cgi-bin/app?mode=display. Sure under the covers it's all the same thing but having that clean namespace can be a blessing when you wish to have some special handler for a particular runmode (the handler can then sit on top of the namespace ala modperl instead of being integrated into the app).