One minor issue is that your regex,

$file !~ m/^[\w-]+(\.[\w-]+)*$/
[download]

will, if I read the regex correctly, consider this:

cns061206
[download]

to be acceptable: it's ending with at least zero strings comprising one dot followed by at least one word character or hyphen. That is, the (/\.[\w-]+)* portion of the regex is successfully matching a null-string. This, you could fix by replacing the final asterisk in the regex by a plus sign.

Something like this may do what you want (note: NOT TESTED)

sub zip {
    (my $cmd, my $dir) = @_[0,1];

    my $count;

    if($cmd eq 'unzip') {
        
        foreach my $file (glob($dir . '/*.gz')){ # get only gzipped fi
+les
                if(system(($cmd, $file)) == 0) {
                    $count++;
                }
                else {
                    warn "Could not $cmd $file\n";
                }
            }
        return $count;
    }
    elsif($cmd eq 'zip') {
        foreach my $file (glob($dir . '/*')) {
            next if $file =~ /\.gz$/;
            next if $file =~ /\.txt$/;
            next unless $file =~ /(\.\w+)+$/; # which will skip files 
+without an extension
            if(system(($cmd, $file)) == 0){
                $count++;
            }
            else {
                warn "Could not $cmd $file\n";
            }
        }
        return $count;
    }
    else {
        warn "Unknown command $cmd\n";
    }
}
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You could also check out Tie:Gzip, PerlIO::gzip, or IO::Uncompress::AnyInflate. Note that I've not used any of these, so I'm not endorsing any one of them.

---

NOTE: akin to what idsfa said about readdir, the glob calls should be probably be moved out of the foreach loop control statements. That is, replace:

foreach my $file (glob($dir . '/*')) {
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and

foreach my $file (glob($dir . '/*.gz'))
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with

my @list = glob($dir . '/*');
foreach my $file (@list) {
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and

my @list = glob($dir . '/*.gz');
foreach my $file (@list) {
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respectively.