I don't think anyone will give you the pro/con break down you want as it is a rather large question. So instead here is what I've used in the past, and what I will be using going forward.
I use to use SQL hardcoded in the DAL. I thought this was fine until the DBAs wanted to play with the SQL. Then you have to dig it out, format it and fire it over to the DBAs. Who will laugh at it and replace it all. But without the nice question marks, or the question marks in the wrong order and leave you to stick it back in the Java code.
We have also used a ORM, and while this is great for developers our DBAs hated it as there is no SQL for them to laugh at. We also used a odd ORM (a custom one from 3rd party supplier) which had a habit of killing the database. I've used JPA since and was great, but getting anything complicated using it past the DBAs is a up hill battle.
We now use Stored Procedures (with the call statement hardcoded). Now the first thing everyone will complain about is that you are tied to the database. You are. However how often have you changed database? I know for a fact that we simply could not even attempt it, the amount of other code dependent on it plus retraining our DBAs plus migrating the data. It would be a very expensive operation. However if in your world changing DBs at a drop of a hat is required SPs are likely out.
Going forward I would like to use stored procedures with code generation tools to create Java classes from Oracle packages.
Edit 2013-01-31: A few years and DBAs later and we now use Hibernate, going to SQL (stored procs in the DB) only when absolutely required. This I think is the best solution. 99% of the times the DBs don't need to worry about the SQL, and the 1% they do it is in a place they are already comfortable with.