I got interrupted or I'd have put this up earlier. This is much like thelonius's solution. I post it only because it shows the queue idea much more clearly.

In this code the line:

    ($cur, $next) = ( $next, scalar( <IN>));
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may be generalized to slide any size window over a stream:

    @queue[0 .. 4 ] = ( @queue[ 1 .. 3], scalar( <IN> ));
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Also I like to setup such a queue going into a loop than clean up a queue when exiting a loop. It seems clearer to me but I can only call that a personal preference.

This code seems to work.

#!/usr/bin/perl -T
use strict;
use warnings;

my ( $input, $unique, $dupe) = qw( input unique dupes );
my $is_dupe;

open( IN, $input )           or die "Can not open $input";
open( UNIQUE, ">", $unique ) or die "Can not open $unique";
open( DUPES, ">", $dupe )    or die "Can not open $dupe";

my $cur = <IN>; 
exit if not defined $cur;

my $next = <IN>;

no warnings "uninitialized";
while ( 1) {
    if ( $cur == $next) {
        print DUPES $cur;
        $is_dupe = 1;
    } else {
        if ( $is_dupe) {
            print DUPES $cur;
        } else {
            print UNIQUE $cur;
        }
        $is_dupe = 0;
    }
    ($cur, $next) = ( $next, scalar( <IN>));
    last if not defined $cur;
}
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