You don't do anything with values from %banned and you don't necessarily do lookups on the keys, so you might as well make it @banned. It is static, so you can define it only once, outside the loop.

Try this on for size,

my @banned = qw(
    at be for and to of in the as it are is am on an you me
    a b c d e f g h i j k l m n o p q r s t u v w x y z
    0 1 2 3 4 5 6 7 8 9 10
);

for (1 .. 20000) {
    open local(*IN),"/var/www/data/$_.txt" or next;
    my $url = <IN>;
    my %count;
    while (<IN>) {
        $count{lc $_}++ for split /\W+/;
    }
    close IN or die $!;

    delete @count{@banned};

    print # all the output stuff
}
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You are churning your wheels a little with some of your output code, but ditching temporary variables and using slices of anonymous arrays will fix that. You can replace reverse sort {foo($a) <=> foo($b)} with sort {foo($b) <=> foo($a)}.