-Use the native SQL for things that hibernate was not really built for like batch queries (it can be done but its not what an ORM is designed for) or in some cases Stored Procedures.
-Prefer Criteria queries for dynamic queries. In this case there is no need to to parse before generating. This makes it superior to concatenating HQL together, using a
string builder (this should be avoided). They are also type safe if you are using the JPA criteria API.
-Named queries are the best performing as they are generated and parsed only once. Use these for frequent queries that are not dynamic. HQL also has the benefit of being easier to read than criteria queries.
-Non-named queries must be parsed and generated each pass, for infrequent queries this is fine, but otherwise I would go with one of the other options.