There are many vcs available. Which of them are typically used in JavaEE world?
There are so many doing Java EE development that - regardless of VCS - you will find some place using it if looking long enough.
These days you either have to conform to existing infrastructure, or you go with the VCS with the best support in your chosen IDE.
If you just want to get started using this, then consider using CVS which is simple, and is well-supported in almost all IDE's. You can then learn how it works, including how to diff an older version etc.