I can't say I have had that much problem with using Perl on IIS 5.1 using pure CGI and perl.exe.

The only problem I can think of is that timeout configuration does not work properly and have to by set under Web Sites->Properties instead for the specific sites.

As far as I know, no really good mod_perl equivalent is available, but FastCGI should work. FastCGI is now officially supported on IIS, but i haven't had a chance to try that yet. http://www.iis.net/fastcgi

What problems are you others referring to? Is there something I have missed that I should be aware of? Security/stability issues for instance?