The most widely used documentation standard for is javadoc
. On javadoc's home page you can also find a link to DocCheck, which allows you to analyze your complete code base for missing javadoc comments and wrong documentation links. It generates nice statistics for you that you can use get an overview about the situation. With this data you could make estimates about how much time you will still need to finish the documentation, or you can focus the effort on more important areas if you find out that you will not have enough time to finish the complete documentation.
And there is always UML. It could be that many companies use UML only for documentation purposes, and not for design. A good book about the topic is "Developing Enterprise Java Applications With J2EE and UML". A good tool is Enterprise Architect
. Enterprise Architect also generates database diagrams directly out of the datasource, and java class diagrams from your code. Of course those diagrams need some manual finetuning. EA is also very affordable.