How you do this is going to be dependant on your web server. For example, on Apache, you're first going to have to install mod_perl and then do edit your httpd.conf to create another default document. But before you do that, you're going to have to allow script execution outside of the cgi-bin dir (or at least that's what I do)..

here's what's in my httpd.conf for that (you should read the mod_perl documentation so you REALLY know what's going on though.)

  <Files *.pl>
    SetHandler perl-script
    PerlHandler Apache::Registry
    Options ExecCGI
  </Files>
[download]

You could also restrict this to just a directory if you wanted. -

  <Location /perl>
    SetHandler perl-script
    PerlHandler Apache::Registry
    Options +ExecCGI
  </Location>
[download]

As far as adding a default page, look for DirectoryIndex..

DirectoryIndex index.html index.htm index.shtml index.php index.php4 i
+ndex.php3 index.cgi index.pl
[download]

And I belive that a spider will request the default page from the root of your site. If that happens to be a script, it will get the results of the script.

Hope this helps..
Rich