Both Eclipse and NetBeans are very good and are widely used by professional Java developers. If you look at the number of users, then Eclipse is bigger than NetBeans. I use Eclipse 3.3 (the Europa release) myself.
It used to be the case that NetBeans had more tools for web development out-of-the-box than Eclipse (with Eclipse, you had to download and install additional plug-ins), but Eclipse now offers different packages - if you download "Eclipse IDE for Java EE Developers" from the download page then you have everything you need to develop Java web applications out-of-the-box.
I have briefly tried NetBeans, and I immediately missed the refactoring tools that I am used to have in Eclipse (for example tools to automatically rename variables, classes, methods etc. across the whole project). I don't know if NetBeans doesn't have the same kind of tools, or if I just didn't find them.