You can use hashes (as the perlfaq4 suggests):

How do I compute the difference of two arrays? How do I compute the intersection of two arrays?

perdoc -q arrays

citromatik

Update:i.e. you can try something like this: (not tested)

my %count = ();
my @tableused = ();
foreach $W (@tableList,@fileList){ $count{$W}++ };
foreach $elem (keys %count) {
    push @tableused, $elem if $count{$elem} > 1;
}
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Update2:Your code seems syntactically valid, except for the equality test:

if($W==$Q)

If you are comparing strings you should use the "eq" op

if ($W eq $Q)