try this:

#!/usr/bin/perl
use strict;

my (%count, $occ);
my @files = ("file1", "file2", "file3");

# read all files sequentially
foreach my $file (@files) {
    open (IN, "<$file") || die "could not open $file\n";
    while (<IN>) {
        chomp;
        # if line contains specified string add it to 'file' and 'foun
+d string' specific array
        /(H\(\d+\))/ && do { push @{$count{$file}{$1}}, $_ }
    }
    close (IN);
}

# loop over files
foreach my $file (keys %count) {
    print "$file\n";
    # loop over found strings
    foreach my $found (keys %{$count{$file}}) {
        # count occurences
        $occ = scalar (@{$count{$file}{$found}});
        # print found lines if occured more than 1 time
        if ($occ > 1) {
            foreach (@{$count{$file}{$found}}) {
                print "$_\n";
            }
        }
    }
    print "\n";
}
[download]

I had 3 files to test with:

file1:
N(8) -- H(15) .. O(9)
N(8) -- H(16) .. N(8)
N(8) -- H(16) .. O(9)

file2:
N(8) -- H(15) .. O(9)
N(8) -- H(15) .. N(8)
N(8) -- H(16) .. O(9)

file3:
N(8) -- H(15) .. O(9)
N(8) -- H(15) .. N(8)
N(8) -- H(16) .. O(9)
[download]

and it looks like:

file1
N(8) -- H(16) .. N(8)
N(8) -- H(16) .. O(9)

file2
N(8) -- H(15) .. O(9)
N(8) -- H(15) .. N(8)

file3
N(8) -- H(15) .. O(9)
N(8) -- H(15) .. N(8)
[download]

Imre