Good news, everyone! (in my best Professor Farnsworth voice)
At least for those amongst us who are into programming their NXT with Java, in particular with leJOS NXJ: there's finally an Eclipse plugin available that in an integrated way allows to upload the firmware and to develop, compile and upload NXT Java programs to the brick in Eclipse (the most popular Java IDE presently around, and justifiably so).
Based on the latest leJOS NXJ release, it supports the most recent Eclipse version 3.3 (Europa), thus runs on Windows and Linux.
Use Eclipse's Update manager to install it from the remote update site as follows:
Name: leJOS NXJ (or whatever you like)
For configuration and usage, consult the leJOS NXJ topic in Eclipse's Help->Help contents view after installation.
Give it a try and provide feedback.