Animated

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

The Complete Collection of Algorithm Animations - A list of links to algorithm animations, primarily Java applets. The list includes an overview of each of the linked algorithms.
www.cs.hope.edu/alganim/ccaa/

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

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

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

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.
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".
www.dis.uniroma1.it/~demetres/Leonardo/

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

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.
opsis.sourceforge.net

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

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