I'm not sure it really matters from a perl perspective.

For simple, low traffic stuff, CGI works well and is supported by most web servers.

If you're serving from a windows box and are using ActiveState's perl you can use ISAPI for better speed on both IIS and the Windows port of Apache.

A similar technique is to use mod_perl for Apache.

I've also heard good things about using Fast CGI to speed things up.

But all those are just protocols to help your web browser and your script communicate. I'd say the bid difference is which web server do you feel most comfortable configuring & maintaining.

Personally I find Apache's text configuration files easier to navigate than trying to remember which of IIS's dialog boxes may have the correct option. But hey, that's just me.