Ok, first thing's first. What you actually want is the Largest Common Contiguous Ordered Subset. And so I give you a somewhat terrible algorithm (STA).

sub find_flccos {
  my @a = @{$_[0]};
  my @b = @{$_[1]};
  my (%map,@curchk,@longest);
  
  foreach my $i (0 .. $#a) {
    # I decided to store this map so we don't repeat this 
    # O(n) step if we come across the same letter again
    $map{$a[$i]} = [ grep $b[$_] eq $a[$i], (0 .. $#b) ] unless define
+d $map{$a[$i]};
    # ok, these are the indices in b where we should 
    #start matching from
    foreach my $j (@{$map{$a[$i]}}) { 
      @curchk = ();
      # make temporary indices
      my ($ti,$tj) = ($i,$j);
      # fill @curchk with the longest current match
      while ($ti < @a && $tj < @b && $a[$ti] eq $b[$tj]) {
        push @curchk, $a[$ti];
        $ti++;
        $tj++;
      }
      # change the longest array if it is longer 
      #than the one found previously
      @longest = @curchk if ($#curchk > $#longest);
    }
  }
  return @longest;
}


__DATA__

my (@a,@b,@c,@d,@e,@f);
@a = qw( a a a a b c d );
@b = qw( a b c b a b a c a d );

@c = qw(fred bob joe jim mary elaine);
@d = qw(frank joe jim mary bob);

@e = @f = ();

print join ",", find_flccos(\@a,\@b);
print $/;

print join ",", find_flccos(\@d,\@c);
print $/;

print join ",", find_flccos(\@e,\@f);
print $/;

OUTPUT:
> perl flccos.pl
a,b,c
joe,jim,mary

>
[download]

Hope this helps.

Update: Looked like a disgusting mess before I put the comments on multiple lines. Sry ;-)

antirice    
The first rule of Perl club is - use Perl
The ith rule of Perl club is - follow rule i - 1 for i > 1