JODE (Java Optimize and Decompile Environment)  
   Can be used to optimize, obfuscate and/or decompile code. [Open Source, GPL]
   http://jode.sourceforge.net/

Condensity  
   Shrinks, obfuscates, and optimizes code, protecting class files from reverse engineering, making them smaller and more efficient. [Commercial]
   http://www.condensity.com/

RetroGuard  
   Highly-configurable Java bytecode obfuscator with support for Java 2, reflection and scripting. [Open Source, LGPL]
   http://www.retrologic.com/retroguard-main.html

CodeShield  
   Command-line obfuscator for Java class files. [Commercial]
   http://www.codingart.com/codeshield.html

JCloak  
   Bytecode obfuscator to protect code from reverse engineering. [Commercial]
   http://www.force5.com/

Smokescreen  
   A Java class file obfuscator, that supports selective renaming, unused method and field removal, as well as bytecode obfuscation. [Shareware]
   http://www.leesw.com/

JProof 1stBarrier  
   Java obfuscation tools provide a convenient way of protecting Java applications and applets from reverse engineering, decompiling and other technology theft. [Commercial]
   http://www.jproof.com/products.html

Marvin  
   Removes unnecessary classes and obfuscates applications, applets, and servlets. Supports encryption of string constants. [Freeware]
   http://www.drjava.de/obfuscator/

Jshrink  
   Removes unused code and data then obfuscates symbolic names in class files. [Commercial]
   http://www.e-t.com/jshrink.html

Zelix KlassMaster  
   Java obfuscator with flow obfuscation, string literal encryption, scripting, Ant integration, incremental obfuscation, obfuscated line numbers, J2ME plugin and stack trace translation. Also removes unused classes, fields and methods. [Commercial]
   http://www.zelix.com/klassmaster/

IBM alphaWorks JAX  
   A Java application packaging tool that reduces the distribution size of a Java application. [Commercial]
   http://www.alphaworks.ibm.com/tech/JAX

jarg - Java Archive Grinder  
   Shrinks and obfuscates jar files. Runs from the command line or as an Ant task. [Open source, BSD]
   http://jarg.sourceforge.net/

JObfuscator  
   A Java obfuscator that uses XML project files and can be easily integrated with Ant build systems and IDEs that support Ant tasks. [Shareware]
   http://www.jobfuscator.com/

ProGuard  
   Shrinks and obfuscates, with template-based configuration. Comes with an Ant task, a J2ME WTK plugin, and a tool to de-obfuscate stack traces. [Open source, GPL]
   http://proguard.sourceforge.net/

JavaGuard  
   Obfuscates. Updated version of RetroGuard. Can be run from the command-line or using a GUI. [Open source, GPL]
   http://sourceforge.net/projects/javaguard/

yGuard  
   Bytecode obfuscator configurable to run through Ant build scripts. [Freeware, core library is open source, LGPL]
   http://www.yworks.com/en/products_yguard_about.htm

jPresto  
   Shrinks and obfuscates code for the J2ME platform as well as the J2SE platform. [Commercial]
   http://www.s5systems.com/jPresto.htm

JZipper  
   Obfuscates and packages required Java class files. [Commercial]
   http://www.vegatech.net/jzipper/

CafeBabe  
   Interactively displays and obfuscates the internals of class files. [Open Source]
   http://www.geocities.com/CapeCanaveral/Hall/2334/Programs/cafebabe.html

JLock  
   A Java class file encrypter. It transparently encrypts Java class files and at run-time decrypts the code, so that the JVM can interpret the class file as a valid Java byte-code. By JBit Software. [Commercial]
   http://www.jbitsoftware.com/JBitSoftware/jlockinfo.html

Cinnabar Canner  
   Protects Java-based applications from decompilation and reverse engineering by embedding an encrypted version of the application's classes and resources into a native Windows executable. [Commercial]
   http://www.cinnabarsystems.com/canner.html

Semantic Designs Java Obfuscator  
   Scrambles source code using nonsense names and stripping comments to disable reverse engineering. Works on large sets of files. [Commercial]
   http://www.semanticdesigns.com/Products/Obfuscators/JavaObfuscator.html

Katirya  
   Encrypts Java class files and create and executable file. At run time, Katirya decrypts class files and delivers valid Java byte-code to class loader to load the class. Req. registration for download. [Shareware]
   http://www.mycgiserver.com/~ipnetdevelop/katirya.html

Saffeine  
   Tool for the Java bytecode protection and feature driven license management. The 'Saffeine' engine uses strong cryptography algorithms to obfuscate unlicensed Java byte code. [Commercial]
   http://www.saffeine.com/

DashO  
   Obfuscates to enhance source code security, shrinks to improve efficiency, and watermarks to track the origin of a pirated copy. [Commercial]
   http://www.preemptive.com/products/dasho/