Refactoring and code tracking and analysis support tool. May be used standalone or integrated with IDEs such as Netbeans, Forte, JDeveloper and JBuilder. [Commercial]
A plugin that adds automatic refactoring of Java source code to the editor. This currently includes class, field, method, and package renaming and push-down and pull-up of methods and fields in an inheritance hierarchy. [Open Source, LGPL]
Tool to automatically restructure (refactor) Java inheritance hierarchies, and delete duplicate code. Such tools are most useful with OO code, more so prototype-based. Brief description, example diagram, links. [Open Source, MIT]
Open source Java refactoring tool, supports a dozen refactorings; command line options: with/without GUI, comes as plugin for IDEs Elixir, JBuilder, NetBeans: in the first two, can now switch from UML diagram to source code. [Open Source, Apache style]