Why making it so complicated? You could use a much simpler regular expression and then remove the quotes later.

#!/usr/bin/perl -w
use strict;

while (<DATA>) {
    chomp;
    print "$_\n";

    if (/-(\S+)(\s*(.*))?/x) {
        my ($p1, $p2) = ($1, $3);
        if (defined $p2) {
            $p2 =~ s/^"//; $p2 =~ s/"$//;
        }
        print "[$p1][$p2]\n";
    }
}



__DATA__
   -libs "source*.lib source*.lib"
   -1dlu
   -2dlu
   -3dlu "(1,1,3)"
   -filter  ASDF
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