The top ones are IntelliJ IDEA, Eclipse and NetBeans. There are a few more like JBuilder, JCreator and the one from Oracle, which is JDeveloper.
The first three are of course widely used and has a big community. Out of these, IntelliJ IDEA is not free, but the other two are. Eclipse and NetBeans are open source projects and are freely available.
I have some experience in all these three IDE's and would like to put down what I think about them.
IntelliJ is the best Java IDE I have seen. It has all the java developer needs, which includes easy configuration, loads of features, good usability. But since it is not free, only few companies consider it in their budget and most companies cannot afford it. But if you can afford it, you will enjoy developing using this IDE.
Then we come down to Eclipse and NetBeans. If we would be discussing a few years back, Eclipse would be clearly a better choice, since NetBeans was not that great. But since NetBeans 6+ was released by Sun, I feel Netbeans has over taken Eclipse in usability and ease of use.
I have used both Eclipse 3.5 and NetBeans 6.7 recently and I was with ease with NetBeans and Eclipse was a head ache while configuration. Eclipse has of course a lot more plugins and some additional features when compared to NetBeans. But, setting up a project and starting to use is much easier in NetBeans. The features available were enough as per my requirement and I did not find a need for more.
Speed wise, I felt Eclipse was faster, as NetBeans takes a long time in scanning through all packages.
If you ask my opinion, I would select NetBeans as configuration has been my weakness and I am worst in that and I get frustrated doing it. NetBeans also comes with a good profiler which is very useful. On other features, there is not much of a difference between Eclipse and NetBeans.
I would say the future for NetBeans looks better than Eclipse. Then again, if you have been using Eclipse for a long time, you should prefer Eclipse.