I had a big pool of really broken code. It was written against a really old version of LWJGL that I no longer had the jars for, was in a strange state as far as commits to the source repository (parts of the code was from the very first commit, others were from the very last, and everything inbetween), some stuff was completely missing, and all in all it was a complete mess.
A long time Eclipse fan, I first attempted to get it stable again in Netbeans 5. But the code being so horribly broken meant Netbeans just couldn't handle it. It crashed often, got really unstable, did weird things like refactorings I asked for would get undone 10 minutes later. I found myself fighting Netbeans a lot more than I was fixing the code. I gave up and went back to Eclipse.
Eclipse handled it no problem. Eclipse seemed more willing to accept the codebase was a pile and was content to let it sit broken and help me fix it wherever it could. With a large help from Eclipse the code is now completely clean, ready to go, and has been the basis of my games for the past month or so.
I can't offer any technical reasons behind what happened here, just as an end user say Eclipse came through and Netbeans didn't. And I still really hate Swing being used for heavy apps, even in OS X. So I'm still an Eclipse user.