We happen to use the iBatis SQL mapper, which is closer to the metal than ORMs like Hibernate. In iBatis you put the SQL statements into resource files (XML), which need to be in the classpath.
Your list of approaches seems pretty comprehensive if you add @ocdecio's ORM option. I would say that using an ORM and using an SQL mapper and resource files are the two best approaches. I'd steer clear from SQLJ, which hasn't seen much uptake and ties you too closely to Java. Also stay away from stored procedures, since they tie you to a specific database vendor (standards are almost non-existent for stored procedures).
