OptimalAdvisor - A tool to analyze and refactor java code. [Commercial, trial Version]. - http://frontline.compuware.com/javacentral/tools/26222.asp
Condenser - 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] - http://condenser.sourceforge.net/
Design Pattern Transformer - A prototype-tool for automatic program transformations, which allows refactoring of programs written in Java language. [Freeware] - http://www.kupin.net/uni/dpt.html
JavaRefactor - JEdit Plugin - 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] - http://plugins.jedit.org/plugins/?JavaRefactor
Transmogrify - A Java code analysis and manipulation architecture. Currently, the focus of the architecture is as a refactoring tool. [Open Source, GPL] - http://transmogrify.sourceforge.net/
Refactorit - Refactoring and code tracking and analysis support tool. May be used standalone or integrated with IDEs such as Netbeans, Forte, JDeveloper and JBuilder. [Commercial] - http://www.refactorit.com/
JRefactory - 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] - http://jrefactory.sourceforge.net/csrefactory.html