You appear to be passing the commands in to the standard input of the program. If there isn't a good reason for that then you can pass them on the command line:

my ($command1, $command2, $command3) = @ARGV;
$command2 = 'default' unless defined $command2;
$command3 = 'hoo hah' unless defined $command3;

# OR

my $command1 = shift or die; # Ideally call a subroutine to print usag
+e and die
my $command2 = shift || 'default';
my $command3 = shift || 'hoo hah';
[download]

If you have to read from STDIN then you can check to see if it still has stuff available using the eof function:

my $command1 = <STDIN>; chomp($command1);
my ($command2, $command3) = ('default', 'hoo hah');
unless (eof(STDIN)) {
    $command2 = <STDIN>; chomp $command2;

    unless (eof(STDIN)) {
        $command3 = <STDIN>; chomp $command3;
    }
}
[download]

-ben