Actually, I use the default settings. But then I typically restart (and sometimes rebuild*) the app server when deploying an application. I also tend to use Eclipse as a glorified text editor rather than as a development environment (I have no patience for wizards that require me to fill in a bunch of forms and click a bunch of buttons when I can just as easily copy/paste some text into a source file). I also do all compiling and deploying in Maven or Ant (I turn off autobuild in Eclipse).
*See the build scripts in the book's source code for how I do this.