Eclipse and NetBeans are both great IDEs, there isn't one that's clearly better than the other - the choice mainly comes down to personal preference. I use Eclipse everyday at work, but I've also played with NetBeans and I was pleasantly surprised at how good it is.
If you have the choice, I'd recommend taking some time to try them both out and see what works best for you.
Both Eclipse and NetBeans are based on platforms that you can use the write your own applications (
Eclipse Rich Client Platform and
Netbeans Platform). Note that NetBeans is based on Swing (the standard Java GUI library), while Eclipse has its own GUI library (
SWT = Standard Widget Toolkit).