Here's a version that preserves the line order within the file while allowing out of order lines (for example, "Group 1" appears on the first and last line below) and making empty lines separating groups optional (for example, there are blank lines within the "Group 5" lines below):

use strict;
use warnings;
my %seen;
print map  { $seen{$_} > 1 ? $_ x $seen{$_} . "\n" : () }
      grep { not $seen{$_}++ }
      grep { !/^\s*$/ } <DATA>;
__DATA__
Group 1
 
Group 2
Group 3
Group 3
Group 3

Group 4

    
Group 5
Group 5


Group 5
Group 5
Group 1
[download]

Running the above program produces:

Group 1
Group 1

Group 3
Group 3
Group 3

Group 5
Group 5
Group 5
Group 5
[download]

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