my @file1 = <FILE1>;
my @file2 = <FILE2>;

# Here is where you would normalize the data. Things like uc, lc, ucfirst, s/\s//g, and the like.

my (%file1, %file2);
$file1{$_} = 1 foreach @file1;
$file2{$_} = 1 foreach @file2;

foreach my $value (sort keys %file1) {
    if ($file2{$value}) {
        print FILE3 "$value\n";
    }
}

##</code><code>##

# Using the same data structures as above ...
foreach my $value (sort keys %file2) {
    unless ($file1{$value}) {
        print FILE3 "$value\n";
    }
}

##</code><code>##

my (%file1, %file2);
$file1{$_}++ foreach @file1;
$file2{$_}++ foreach @file2;