BY CGI, I am going to guess that you really mean PERL. The two really aren't the same.
If you install ActivePerl on the server most will work "right of the box". The ones that need modifications are those that use file locking (flock() and funlock()) and those that use the Unix sendmail utility. You can find PERL scripts that run on NT by going to The CGI Resource Index.
You will also find that they have CGI programs written in many other languages like C, C++, Java, Visual Basic and TCL as well.
Since your going to be on NT, you might look into using ASP. I recommend this for several reasons. The most dominate of them are that ASP is faster than PERL and that its easy to use databases, not flat file databases used in PERL but real SQL databases like Oracle, Sybase and SQL Server. You can find ASP scripts to fit any need at ASPIN.