JFLAP, JAWAA, jeLLRap -- Visual and Interactive Tools  
   Tools (Java programs) for visualizing and interacting with theoretical computer science concepts. JAWAA is a tool for creating algorithm animations on the web.
   http://www.cs.duke.edu/~rodger/tools/tools.html

Leonardo  
   An integrated C programming environment for reversible execution and logic-based software visualization developed at the University of Rome "La Sapienza".
   http://www.dis.uniroma1.it/~demetres/Leonardo/

3 Sorts of Sort CAL Package  
   Several sorting algorithms explained using a nice playing card based interface.
   http://www.csis.ul.ie/modules/cs4111/3sorts/

Sorting Algorithms  
   Visualizations of some comparison based sorting algorithms.
   http://www.scs.carleton.ca/~morin/misc/sortalg/

Opsis  
   A Java applet designed to teach binary search tree algorithms. It is unique in the way it combines programming, proof, and animation to enhance the learning experience.
   http://opsis.sourceforge.net

The Complete Collection of Algorithm Animations  
   An extensive list of links to algorithm animations, primarily Java applets. The list is organized by site and by algorithm. [Not recently maintained.]
   http://www.cs.hope.edu/~alganim/ccaa/

Hope College Animations  
   Online animations of algorithms and data structures.
   http://www.cs.hope.edu/~alganim/

LYDIAN  
   Simulation and visualization environment for distributed algorithms that provides students with an experimental environment to test and visualize the behaviour of distributed algorithms.
   http://www.cs.chalmers.se/~lydian/

Backtracking  
   A combinatorial puzzle is presented making visible the performance of a backtracking algorithm (requires JavaScript).
   http://www.faust.fr.bw.schule.de/mhb/backtrack/backtren.htm

Java Applets for Data Structures and Algorithms  
   Demonstrate fundamental concepts in Data Structures and Algorithms.
   http://www.cosc.canterbury.ac.nz/people/mukundan/dsal/appldsal.html

CATAI  
   A distributed algorithm animation system. Algorithms are coded in C++ and the resulting animations displayed using lightweighted java application. Multi user and interactive animations are supported through the use of a distributed CORBA based architectu
   http://catai.dia.unisa.it/

Java Interactive Software Visualization Environment  
   JIVE is an object-oriented general-purpose animation system for the visualization of Java coded algorithms. Visualizations can be embedded in a Java browser or attended in a Virtual Classroom by several users at once.
   http://jive.dia.unisa.it/

Graph Animations with Combinatorica  
   Animations of several important graph-theoretic topics and algorithms.
   http://www.cs.sunysb.edu/~skiena/combinatorica/animations/

Zeus  
   An algorithm animation system developed at Digital Equipment Corporation's Systems Research Center.
   http://www.research.compaq.com/SRC/zeus/

ZADA  
   Interactive graphical (and some audiovisual) Zeus-based animations of distributed algorithms and communication protocols.
   http://www4.cs.uni-dortmund.de/RVS/zada.html

Sort Algorithms Visualizer  
   Applet and web site for teaching sort algorithms. Includes animation of 11 algorithms and some in-depth studies.
   http://thomas.baudel.name/VisuTri/