jFactor  
   Product family of refactoring Java browsers: for professional Java development environments such as IBM VisualAge Java. [Commercial]
   http://www.instantiations.com/jfactor/

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

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/

SD Times: jFactor Speeds Code-Improvement Process  
   Instantiations refactoring tool helps meet enterprise standards.
   http://www.sdtimes.com/news/025/story7.htm

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/

Xref-Technologies - Xrefactory  
   A professional development tool for Emacs and XEmacs with intellisense code completion, source browsing and refactoring functions. It was the world's first C and Java refactoring tool. [Commercial]
   http://xref-tech.com/speller/

OptimalJ - Package Structure Analysis Tool  
   A tool to analyze and refactor java code. [Commercial, free Beta].
   http://javacentral.compuware.com/pasta/

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

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

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/