The answers are commonly found in Java books.
cloning: If you don't override clone method, the default behavior is shallow copy. If your objects have only primitive member variables, it's totally ok. But in a typeless language with another object as member variables, it's a headache.
serialization/deserialization
$new_object = unserialize(serialize($your_object))
This achieves deep copy with a heavy cost depending on the complexity of the object.