From my understanding:
Java serialisation
Advantages
- (+) Java built-in.
- (+) Does not require any coding.
Disadvantages
- (-) May not be compatible between different versions of Java and can not be used in ther languages.
- (-) Can be large.
POF serialisation
- Advantages
- (+) Can be smaller.
- (+) Not reliant on Java, can be used in different versions of Java and other languages.
- Disadvantages
- (-) Extra methods must be coded: extra work and can lead to errors.
- (-) Format and coding can get complicated for complex structures.
Also, you could look at the various serialisation schemas: JSON, XML, Protocol Buffers, Avro, Thrift, etc. In longer term, they may offer these advantages:
- Cross-language support.
- Built-in serialisation/deserialisation.
- External support of the project.
- Protocol Buffers has a number of utilities written for it (including conversion to JSON, XML, etc.). See: Third-Party Add-ons for Protocol Buffers.