1. Programs to Build Models and Simulations

Active Worlds: The Active Worlds Universe is a community of hundreds of thousands of users who chat and build 3D virtual reality environments in millions of square kilometers of virtual territory.
Alice: Alice is an innovative 3D programming environment that makes it easy to create an animation for telling a story, playing an interactive game, or a video to share on the web.
Excelets: Excelets are interactive Excel spreadsheets or simulations of mathematical models.
Google SketchUp: Google SketchUp is software that you can use to create, modify and share 3D models.
Molecular Workbench: The Molecular Workbench (MW) is a free, open-source tool that delivers visual, interactive simulations for teaching and learning science.
Multiverse: Multiverse enables development teams to create high-quality, unique, and engaging virtual worlds and MMOGs faster and for less cost than ever before.
RasMol: RasMol is a program for molecular graphics visualisation.

Notes on getting started with RasMol.
Scratch: Scratch is a new programming language that makes it easy to create your own interactive stories, animations, games, music, and art -- and share your creations on the web.
Squeak: Squeak is a modern, open source full-featured implementation of the powerful Smalltalk programming language and environment.
Stencyl: Create Flash-based games for PC or Mac for free.

2. Systems Thinking/Systems Dynamics
CC Modeling Systems: This website contains information on how to incorporate systems dynamics modeling in the K-12 classroom.
Creative Learning Exchange: The Creative Learning Exchange encourages an active, learner-centered process of discovery in K-12 education that challenges preconceptions, deepens conceptual understanding, and engages in meaningful, real world problem solving through the mastery of systems thinking and system dynamics modeling. (free)
Maryland Virtual High School: The mission of the Maryland Virtual High School is to provide resources for and training in the use of modeling and visualization tools for inquiry based instruction in science and mathematics. (free)
STELLA: STELLA® offers a practical way to dynamically visualize and communicate how complex systems and ideas really work.
Waters Foundation : The mission of the Waters Foundation is to increase the capacity of educators to deliver student academic and lifetime benefits through the effective application of systems thinking concepts,habits and tools in classroom instruction and schools improvement.

3. Multiple Subject Collections of Models and Simulations

BBC - KS2 Bitesize: Simulations in English, Math, and Science for primary students. (free)
Crickweb: 206 free educational interactive resources for Primary Schools. 30 free to use fun games for kids aged 4 - 11. 120 plus links to free interactive, image and software resources.
Crocodile Clips/Yenka/Absorb Courseware: Crocodile Clips develops and sells educational software for schools and colleges. (free/subscription)
ExploreLearning: Online simulations that power inquiry and understanding. (free trial)

A listing of Gizmos available for physics compiled by Kenny Grime of Norfolk (VA) Public Schools.
Falstad: Educational java applets to help visualize various concepts in math, physics, and engineering.
Game Classroom: Educational Games, Worksheets & Homework Help for K-6 Students, Parents and Teachers
Interactives: "Interactives" provides educators and students with strategies, content, and activities that can enhance and improve students' skills in a variety of curricular areas. (free)
Maryland Virtual High School: The mission of the Maryland Virtual High School is to provide resources for and training in the use of modeling and visualization tools for inquiry based instruction in science and mathematics. (free)
MERLOT: Multimedia Educational Resource for Learning and Online Teaching.
Multimedia Gaming: A wiki page containing an extensive list of multimedia education games.
NetLogo Models: This collection of models submitted by users contains everything from voting simulations to fire modeling to predator/prey relationships.
NOVA Interactives Archive: The producers of the PBS science show, NOVA, have posted a gallery of online experiments. (free)
Phet - Physics Education Technology: Science (not just physics) and math simulations. (free)
Playing with Time: Playing With Time is a project that looks at how the world around you is changing over many different time periods.
Shambles: Simulations and games on many topics, including economics, science, and math. Teachers might want to mine this site and share specifics with students--some sites are not classroom-ready (but none are inappropriate).
Shodor: Our Mission: To advance science and math education through the use of computational science, modeling and technology. (free)
Simulation and Virtual Learning Portaportal: A collection of links to simulation and virtual learning web sites.
skoool Sri Lanka: skoool Sri Lanka is a vast educational resource for teachers to use inventively and creatively in the classroom to add extra value to their classroom teaching of Maths and Science.
TechTrekers: A collection of links to simulations in math and science.
The Connected Classroom: Another wiki with links to online resources
Virtual Learning - The 25 Best Sims and Games for the Classroom: College@Home blog
Wolfram Demonstration Project: The Wolfram Demonstrations Project is an open-code resource that uses dynamic computation to illuminate concepts in science, technology, mathematics, art, finance, and a remarkable range of other fields. All Demonstrations run freely on any standard Windows, Mac, Unix, or Linux computer. Anyone can preview a Demonstration online, and interact with it using the free Mathematica Player. Those with Mathematica can also experiment with and modify the code on their own computers.
Zondle: Zondle contains thousands of free games for learning that span all grade levels.

4. Math Models and Simulations

Arcytech: Educational Java programs
Flexcel : Flexible interactive Excel workbooks for math teachers
Center for Technology and Teacher Education: Interactive Mathematics Projects using Macromedia Flash.
GeoGebra: GeoGebra is a free and multi-platform dynamic mathematics software for schools that joins geometry, algebra and calculus. It received several international awards including the European and German educational software awards.
Hands-On Banking: The Hands on Banking program offers basic money tools, skills, and information you need to manage your money.
Illuminations/NCTM: Explore our library of 103 online activities that help to make math come alive in the classroom or at home.
Many Eyes: At this web site, you can upload data and visualize it.
Math Playground: Practice math skills and play logic games.
Math Teaching and Learning Resources: free online resource listing from the federal government. Contains links to many on line models, simulations, and visualizations.
National Library of Virtual Manipulatives: The National Library of Virtual Manipulatives contains computer-based mathematical manipulatives and interactive learning tools for the elementary and middle school level. The Utah State University team developed Java-based mathematical tools and editors that allow interactive mathematical instruction. They are available for free via the Internet or can be purchased on a CD as a desktop application.
Powers of 10: Powers of Ten is an extremely valuable tool for teaching and understanding our world through the concept of scale.
Probability Simulations: Flash movies simulate typical probability experiments. The simulations can be left running to produce thousands of trials.
Shodor Interactivate: A set of interactive online materials for math education for grades 3 through 12.
WisWeb: Wisweb is a digital web-based math environment in which applets are part of the instructional module. This site contains resources for algebra and geometry teachers.

5. Science Models and Simulations

Amazing Space: Get to know our vast universe by exploring its planets, galaxies, comets, black holes, and more.
AP Physics: Simulations designed for AP physics classes
Biology Corner: A resource site for biology and science teachers.
Carbon Footprint Quiz: Calculate the impact you have on the planet.
CAST 2008: The Pittsburgh Supercomputing Center (PSC) presents a program for high school science teachers in western Pennsylvania to prepare them to become leaders in the effective use of modeling and simulation tools in the classroom. The CAST program proposes to bring to the classroom the same problem-solving, technology-rich approaches currently used in scientific research and in business.
Cells Alive: Interactive cell models, including mitosis, meiosis, and cell cams.
Cells (the Virtual Cell): Interactive model of a cell.
Cell Animations: Animations of cell biology.
Center for Technology and Teacher Education: Curry Science Education Program Collection of Simulation Web Sites.
ChemCollective: The Chemistry Collective is a collection of virtual labs, scenario-based learning activities, and concepts tests which can be incorporated into a variety of teaching approaches as pre-labs, alternatives to textbook homework, and in-class activities for individuals or teams. It is organized by a group of faculty and staff at Carnegie Mellon University for college and high school teachers who are interested in using, assessing, and/or creating engaging online activities for chemistry education.
Chemistry Animations and Simulations: A listing of chemistry animations and simulations assembled by the Chemical Education research group at Iowa State University.
ChemSense: ChemSense is software and curriculum developed to help students investigate chemical systems and express ideas in animated chemical notation. The software is available for download free of charge at the web site.
Climate Challenge: A game where you are president of the European Nations. You must tackle climate change and stay popular enough with the voters to remain in office.
Cloning This web site by the University of Utah uses interactive simulations to teach students about cloning.
Computational Resources for Teachers: a collection of modeling and visualization activities for science classes.
EdGCM - Educational Global Climate Modeling: The EdGCM Project develops and distributes a research-quality global climate model (GCM) with a user-friendly interface that runs on desktop computers.
Edheads: Edheads helps students learn through educational games and activities designed to meet state and national standards.
Essentials of Geology: Geology animations
Exploratorium: Online science activities
Froguts.com: Virtual frog dissection. (demo version)
Funderstanding Rollercoaster: It is your mission to design the coaster so that you can achieve maximum thrills and chills without crashing or flying off the track.
Get Body Smart: An Online Examination of Human Anatomy and Physiology
Geology Labs On-line: Geology Labs On-Line was initiated to develop Web-based activities which enhance the learning and teaching of earth science. With these activities, students complete a sequence of tasks that require observation, measurement, and data analysis.
GeoMapApp: GeoMapApp is an earth science exploration and visualization application that is part of the Marine Geoscience Data System (MGDS) at the Lamont-Doherty Earth Observatory of Columbia University. The application was created for the discovery, exploration, manipulation, visualization and analysis of a large choice of built-in and user-imported marine-based data sets.
Golems Golems is a 3D Physics and Artificial Intelligence simulator. Golems lets you construct a machine - any type of machine - and then bring that machine to life.
Google Body Browser Google's new tool for exploring the structure of the body.
HHMI Virtual Labs: Virtual Labs Series produced by the Howard Hughes Medical Institute
JASON Science : The JASON Project connects students with great explorers and great events to inspire and motivate them to learn science. The site has curriculum, digital labs, and games.
Kinetic City: Game interface science experiments.
Learning Science: A collection of tools for teaching science, organized by grade level
Life in Space: Discovery Channel Online simulations of life in space.
My Physics Lab: Interactive simulations animate in real time.
Nobel Prize games: Activities inspired by Nobel Prize winners (includes blood typing, Pavlov's dog, and other simulations)
NASA Online(physical science): Flash player simulations.
NASA Space Place: Come on in and check out our games, animations, projects, and fun facts about Earth, space and technology.
NOAA Environmental Visualization Lab: The Environmental Visualization Laboratory provides images, animations, and Google Earth files depicting weather and climate patterns.
NTNUJAVA Virtual Physics Laboratory: Java simulations in physics (free registration required)
Nucleotide Building Interaction: Click and drag to build nucleotides.
Peppered Moth (camouflage) simulation: Part of Biology Corner
Physical Science Simulations: science simulations "for displaying things that you can not see such as molecules, or for simulating physical situations that you can not bring into the lab"
Physics 2000: An interactive journey through modern physics! Have fun learning visually and conceptually about science and high-tech devices.
Population Biology: Java simulations for teaching principles of population genetics and population ecology
Prentice-Hall Middle School Science: sites tied to Prentice-Hall's middle school science series
Probe the Brain: "We give you an electric probe and an exposed brain. All you need to do is shock and observe."
rayslearning.com: Chemistry software and science teaching resources.
Science Kids: Learn more about the amazing world of science by enjoying our fun science experiments, cool facts, online games, free activities, ideas, lesson plans, photos, quizzes, videos & science fair projects.
Science Teaching Resources: Free online resource listing from the federal government. Contains links to many on line models, simulations, and visualizations.
Science U: Interactive exhibits, animated explanations and science graphics
Secchi Disk Simulation: This simulation allows students to see how a Secchi Disk works in a variety of water conditions.
Technology Enhanced Learning in Science (TELS): TELS curricula incorporate interactive software and simulations that guide students’ work so that they learn to use scientific inquiry as they examine complex topics in science. It is part of the WISE project (link below).
The River City Project: Based on authentic historical, sociological, and geographical conditions, River City is a town besieged with health problems. Students work together in small research teams to help the town understand why residents are becoming ill.
Virtual Microscope: A virtual microscope created by the University of Delaware.
Virtual Tornado: Control the intensity of a twister by changing the diameter and/or the core pressure difference.
Visualizing the Seasons: An interactive simulation of the Earth's seasons.
WISE: WISE (Web-based Inquiry Science Environment) is a simple yet powerful learning environment where students examine real world evidence and analyze current scientific controversies. The curriculum projects are designed to meet standards and complement current science curricula.
World Wide Telescope: WorldWide Telescope (WWT) enables your computer to function as a virtual telescope, bringing together imagery from the best ground and space-based telescopes in the world. Experience narrated guided tours from astronomers and educators featuring interesting places in the sky.

6. Social Science/History Models and Simulations

Code Red Rover: safety activities for middle schoolers and younger students
Ellis Island Virtual Tour: Interactive tour of Ellis Island and information about immigration.
From Ellis Island to Orchard Street: Students play the role of an immigrant to New York City in 1916.
Jim Crow Laws: "interactive modules to challenge and motivate students to learn more about this period in history"
Monticello Virtual Tour: Tour Thomas Jefferson's home and see his inventions.
Rome Reborn: "Rome Reborn is an international initiative whose goal is the creation of 3D digital models illustrating the urban development of ancient Rome"
US History: Virtual tours, documents, activities about US History, hosted by the Independence Hall Association