If I have a command line like:
my_script.pl -foo -WHATEVER
My script knows about --foo, and I want Getopt to set variable
I think the answer here, sadly though, is "no, there isn't a way to do it exactly like you ask, using Getopt::Long, without parsing @ARGV on your own." Ether has a decent workaround, though. It's a feature as far as most people are concerned that any option-like argument is captured as an error. Normally, you can do
GetOptions('foo' => \$foo)
or die "Whups, got options we don't recognize!";
to capture/prevent odd options from being passed, and then you can correct the user on usage. Alternatively, you can simply pass through and ignore them.