Hows this?

my %keys;
while(<>)
{
  chop;
  $keys{$_}++;
}

foreach my $k ( keys %keys )
{
  print "$k: $keys{$k}\n";
}
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This will count the times a particular input line was seen and then print them out in no apperent order. A sort could be added to the foreach if you would like an order, like, for example sort { $keys{$b} <=> $keys{$a} } ... if you wanted them in descending order by count of duplicates.

Update: Also note that this stores only the comparison data and makes only a single pass through the files.