Eclipse is the open source project initiated by IBM, and free of charge. Its advantage is that this IDE is extensible as it allows you to install plug-ins. MyEclipse has a lot of cutomization based on Eclipse, which saves your time to download plugins and installation time. But MyEclipse needs annual subscription fee, which is around US$30 per year. I used MyEclipse for a year, after getting familiar with the user interface, I switched to use Eclipse. e.g. In MyEclpse, you can just add Struts feature by clicking a web project and select add struts. But in Eclipse, at least in v3.3.1, it has no this feature, you have to download a blank.war from struts web site, and add struts feature.
For Netbeans, it is IDE owned by Sun microsystem, also, free of charge as Sun opens its source to the public and allow any people in the world to enhance it. It is pretty cool but its user interface is quite different from Eclipse. The initial launch is pretty slow when compared with Eclipse.
Frankly speaking, at this moment, more developers prefer using Eclipse. For the future, who knows?
Hope this can help you.
P.S. I spent quite a long time to try and getting familiar with these tools. You may surf Netbeans and Eclipse website to find out more.