This might be a little better.

my $temp;
while (($entry,$temp) = each %my_hash) {
  foreach $timeStamp ( sort keys %$temp) {
    my @tskeys = sort keys %{$temp->{$timeStamp}};
    print $Hentry "$entry\t$timeStamp\t", scalar @tskeys;
    print $Hentry "\t$_\t", $my_hash{$entry}{$timeStamp}{$_} for @tske
+ys;
    print $Hentry "\n";
  }
}
[download]

What I've done here is factor out the repeated call to keys on %{$temp->{$timeStamp}} and turned the foreach my $id loop into the statement modifier form. The lack of a block might be faster.