OK, some additional remarks after your problem is solved - as always, there's room for improvement:

• use strict and warnings - this was already suggested but it's important so I repeat it :)
• Substitute all the uses of local and use my instead. For further reading I strongly recommend Coping with Scoping by Dominus. I suspect the snippets you used to put this together were old and came from the time before my ...
• Use getopts instead of getopt and use the hash variant of the function call. These recommendations are not really necessary in this simple program but are in general a good idea (for the differences read up in the Getopt::Std documentation).
• Don't do nested greps, you can chain the tests together with &&

Here is my adapted version to show how these things look like:

#!/usr/bin/perl
use strict;
use warnings;

use Cwd;
use Getopt::Std;

my %opts;
getopts('d:', \%opts);
my $start_dir = $opts{d};
$start_dir = getcwd() unless defined ($start_dir);

listDir($start_dir);
print ("\n\nfinished.\n\n");

sub listDir {
    my $thisdir = $_[0];
    print "\n$thisdir:\n";

    opendir THISDIR, $thisdir;
    my @allentries = readdir THISDIR;
    my @directories = sort grep(-d "$thisdir/$_" && !/^\.\.?$/, @allen
+tries);
    closedir THISDIR;

    foreach my $entry (@allentries) {
        print "\t$entry\n";
    }
    foreach my $entry (@directories) {
        chomp($entry);
        listDir("$thisdir/$entry");
    }
}
[download]

-- Hofmator