Here's somewhere to start. Completely untested code, I just threw this together in the reply textarea :). It may not work at all or it may have glitches. Give it a shot if you will, change whatever you may wish. I'd say that the definition of a "word" your regex uses could use some fixing.

my @banned = qw(
   a at be for and to of in
   the as i it are is am on
   an you me
);

push( @banned, 0..10, 'a'..'z' );

my %banned;
@banned{@banned} = undef;

for my $file (0 .. 20000) {
   open( my $in, '<', '/var/www/data/' . $file . '.txt' )
      or die "open failed: $!";
   open( my $out, '>', '/var/www/sorted/' . $file . '.txt' )
      or die "open failed: $!";

   my %seen;
   while ( chomp( my $line = <$in> ) ) {
      for my $word ( split( /\W/, $line ) ) {
         $word = lc( $word );
         ++$seen{$word} if ( exists( $banned{$word} ) );
      }
   }

   my @frequent = (
      sort { $seen{$b} <=> $seen{$a} } keys %seen
   )[0..50];

   print $out join("\n", @frequent);

   close( $in ) or die "close failed: $!";
   close( $out ) or die "close failed: $!";
}
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