Animated

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/

Backtracking - A combinatorial puzzle is presented making visible the performance of a backtracking algorithm (requires JavaScript).
http://www.hbmeyer.de/backtrack/backtren.htm

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/Visualisation/VisuTri/

Java Applets for Data Structures and Algorithms - Demonstrate fundamental concepts in Data Structures and Algorithms.
http://www.cosc.canterbury.ac.nz/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.
http://www.cs.duke.edu/~rodger/tools/tools.html

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/

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/

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

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