CGI::Application is meant to be subclassed. This means that you're supposed to write a class that uses it as a starting point. When I write C::A apps, I actually have 2-3 levels of baseclasses. The first one is my global baseclass. It's my version of what C::A should do. This includes providing a print() method that dispatches between HTML::Template, Excel::Template, and PDF::Template. I see no reason why you shouldn't go ahead and provide a param()-type method in your global baseclass that will untaint the parameters as you need them. You could even link it with CGI::Untaint as so:

sub cgiapp_prerun {
    my $self = shift;

    $self->param( handler => CGI::Untaint->new( $self->query->Vars ) )
+;

    return $self->SUPER::prerun( @_ );
}

sub extract {
    my $self = shift;
    my ($method, $name) = @_;

    my $handler = $self->param( 'taint_handler' );

    return $handler->extract( $method => $name );
}
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Now, your calls to $self->extract() are wrappers around CGI::Untaint's extract(). Done.