I suggest that you create a hash to store the number of times you have seen something. Then, you can iterate over the hash to create the output.

Updated: So, I was a little behind on this and basically solved it the same way as other monks. Oops. That's what happens when your boss walks in while you are playing around on PM. :)

use strict;

open (IN, "test.txt")   or die "Can't open file: $!";
open (UNQ, "> unq.txt") or die "Can't open file: $!";
open (DUP, "> dup.txt") or die "Can't open file: $!";

my %hash;

while (<IN>) { chomp; $hash{$_}++; }

foreach (keys %hash) {
  if ( $hash{$_} > 1) { print DUP "$_\n"; }
  else { print UNQ "$_\n"; }
}

__END__

fraser:~$cat test.txt
0000
1111
2222
3333
4444
0000
3333
1111
5555
1111
0000
0000
1111
3333
6666
0000
fraser:~$cat unq.txt
6666
4444
2222
5555
fraser:~$cat dup.txt
0000
3333
1111
fraser:~$
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</ajdelore>