You could use backticks(`) to capture the STDOUT of the nslookup, and then write to the files w/o storing them in an array. Maybe something like this.

open(OURS, '>/path/to/ours');
open(THEIRS, '>/path/to/theirs');
open(UNKNOWN, '>/path/to/unknown');

foreach my $line (@domain) {
  chomp $line;
  print "running whois on $line\n";
  my $output = `$cmd $line`;
  if(#ours){
    print OURS "$line\n";
  }elsif(#theirs){
    print THEIRS "$line\n";
  }else{
    print UNKNOWN "$line\n";
  }
}

close(OURS);
close(THEIRS);
close(UNKNOWN);
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