I think perhaps you're confusing the abilities of Perl with something like JavaScript. In a CGI/web server environment, Perl scripts execute on the server, and simply return content to the browser. JavaScript can be a part of that content, but is always executed on the browser side. That's how JavaScript can affect the behavior of the browser; the browser is the one executing the code. Perl can't do that, because the browser never sees the Perl code. All the browser gets is the output of the Perl script.

The other posts in this thread should help you on your way. There's no reason window.open() shouldn't work with dynamic code, and simply specifying a target="..." attribute for certain tags will put content in other windows without needing to explicitely create them using JavaScript. Either of these techniques should work across browsers (though if they don't have JavaScript enabled...)