Maybe when you work with several (many) projects at the same time I would prefer Eclipse (Workspace organization is great for that). Interface seems to respond better (at least vs old versions of NetBeans such as 5.0) in Eclipse too. This is related to SWT vs Swing performance issues, though the differences are no so big as on Java 1.4 days.
However I would say Netbeans is a better integrated IDE, you launch/debug applications the same way no matter you are developing a desktop application or a JSP/Servlet web application. Building relies entirely (since version 4 I think) on Ant, and Netbeans launches/adds ant target transparently. Ant in Eclipse has the same level of integration as a pair of bull horns sticked to the front of your car.
Eclipse is more extensible than Netbeans but the last is more uniform.