A long time I invested to explore the project called Datanucleus where you can use object oriented DBs like db4o, relational DBs like derby or just XML files as datasource!
Thats fantastic and open source🙂. You can find more implementations of JDO here.
Derby is a good database, which could pass ACID tests. You could run it in embedded mode, which makes it suiteable for the usage in your standalone swing application.
A pure xml library is XStream. Where you can (de)serialize your objects with one method call. No configuration! Really.