foreach my $gene ( @{ $first_clone->get_all_Genes() } ) {
    print $gene->stable_id(), "\n";
}

##</code><code>##

my $gene_ref= $first_clone->get_all_Genes();
foreach my $gene (@$gene_ref) # or (@{$gene_ref}), the same.
                              # extra {} only needed 
                              # when subscript is used
{
   print $gene->stable_id(), "\n";
}

##</code><code>##

my $genes = $first_clone->get_all_Genes();
while ( my $gene = shift @{$genes} ) {
    print $gene->stable_id(), "\n";
}