Apache web server is better to use with Perl because:

• Apache web server is open-source
  (you can customize it to your CGI needs, Interface Perl with a wider array or open-source applications
  which provide more benefits or scope, get access to more documentation and support more easily)
• It is available for multiple platforms. (speaks for itself)
• Apache is easily scalable as compared to IIS
  (you can run it and Perl on lesser resource specs and still acheive good performance)
• It isn't Microsoft
• It's free. And so is Perl.

Haven given all these general points about why HTTPD is better than IIS which may or may not completely relate
to CGI itself. Please note that I have never benchmarked the 2 web servers on any tests (including CGI Perl or mod_perl). And you may think I am biased. That's probably because I am. But for good reason.

I guess that running Perl with Apache on Linux/UNIX is a good match cause of the nature of the Perl API. But there is no reason to not run Perl on a Microsoft box. Perl can run on anything. Apache just knows more about Perl than IIS. I could be completely wrong in any of my points and I am not qualified to comment really. But still. I just had to reply :)