Nice answer, ++blakem! Let me make some small remarks - your code has slight differences to the specifications ...

• next if /^\s*[#*]/; # comments start with # or *
• $curroption = $1 if s/^([A-Z]+) //;GroundZero is matching the option case insensitive - but this would break your code and you would have to resort to the comma-at-end-of-line solution suggested by grinder. As I understood the problem, the options (like on, except, ...) are known beforehand. In that case your elegant solution is easily fixable:

  # at top of program
  my @options = qw/on except some more options/;
  my $opt_string = join '|', @options;
  my $opt_pattern = qr/^($opt_string)\s+/i;
  
  # instead of your line
  $curroption = $1 if s/$opt_pattern//;
  [download]

  and everything should be fine - as long as the option keywords are not allowed as values for any of the options.
• push accepts a list: push @{$options{$curroption}}, split(/,\s*/);
• Instead of the for loop I'd use a while (each) construct:

  while (my ($option, $val_ref) = each %options) {
      print "$option -- ", join (',',@$val_ref), "\n";
  }
  [download]

-- Hofmator