Basically, command line parameter/switch handling is no different under Perl2Exe than it is under Perl itself (perl.exe). All command line parameters are collected in the @ARGV array and there are modules like Getopt::Long that help you conveniently separate switches, values and parameters.

Personally, I discourage you from using Getopt::Std, because it was written by TheDamian for his book Perl Best Practices and has seen no widespread use outside of that. ¹ Getopt::Long, together with Pod::Usage is what I use to handle documentation and command line switches.

Update: ¹ I was thinking of Getopt::Euclid resp. Class::Std, neither of which are recommendable IMO.