Below is a collection of simulations and games for learning about Earth science that educators at the UCAR Center for Science Education have tried and recommend. Also check out the Learning Zone Games and Simulations

BrainPop GameUp

BrainPop GameUp

BrainPop hosts many educational animations and other resources. The GameUp section of BrainPop offers free games, many covering science topics, including: Hot Air Balloon, Wind Simulator, Carbon Cycle, Nitrogen Cycle, Water Cycle, Magnet Hunt, and many more.

Creators: games on BrainPop come from various sources, including Field Day Lab, Spongelab Interactive, PhET, and others.
Cost: the GameUp section is free; access to other resources on BrainPop requires a paid subscription
Climate Interactive: Tools

Climate Interactive - Tools

Climate Interactive has a suite of interactive computer simulations and role-playing games covering climate, energy, and systems-thinking topics. Includes C-Learn, Climate Pathways App, World Climate, World Energy, Climate Bathtub Animation, and more..
Creators: Climate Interactive and MIT's Sloan School of Management.
Cost: free

Disaster Dynamics game

Disaster Dynamics: Hurricane Landfall

Disaster Dynamics: Hurricane Landfall is a multiplayer, role-playing strategy game that teaches about interactions between natural hazards and human decisions in a Gulf Coast barrier island community..
Creators: National Center for Atmospheric Research (NCAR).
Cost: free

EarthGames from U. Washington

EarthGames at U. Washington

EarthGames has produced several computer-based and tabletop games relevant to the atmospheric sciences, climate, and ecology including: Infrared Escape, Climate Quest, AdaptNation, Erode Runner, A Caribou's Tale, and EcoTrivia..
Creators: researchers, game developers and students at the University of Washington.
Cost: free

Extreme Event Role-playing Game from Koshland Science Museum

Extreme Event Role-playing Simulation

Role-playing simulation for groups in which players assume roles as city leaders to prepare for and react to a natural disaster. Two scenarios: coastal city struck by hurricane or inland city with river flooding. Low-tech and high-tech (using laptops or tablets) variants available; also uses cards..
Creators: Koshland Science Museum.
Cost: free

Gizmos by ExploreLearning

Gizmos by ExploreLearning

ExploreLearning has created hundreds of simulations for math and science, primarily for students in grades 3-12 (also some college-level). Science simulations cover a range of subjects, with largest collections in physics. Atmospheric science titles include: Greenhouse Effect, Relative Humidity, Hurricane Motion, Seasons, Weather Maps, Coastal Winds and Clouds, and more.
Creators: ExploreLearning.
Cost: commercial product - contact ExploreLearning for pricing

MetEd collection by COMET

MetEd by COMET

The MetEd collection includes hundreds of graphics, animations and lesson modules for weather and atmospheric science education. 
Creators: The COMET Program at UCAR
Cost: free, registration required

Monash University Simple Climate Model

Monash Simple Climate Model

A full climate model, simplified for educational use. Includes numerous example scenarios and challenge exercises for students; some involve depictions of alien worlds from science fiction movies and books!
Creators: Dr. Dietmar Dommenget and colleagues, School of Earth, Atmosphere & Environment, Monash University, Melbourne, Australia
Cost: free

NASA Climate Kids - games

NASA's Climate Kids

The games section of NASA's Climate Kids web site includes Wild Weather Adventure, Whirlwind Disaster, Weather Slyder, Cloud Picture Scrambles, and Earthy Word Games.
Creators: NASA
Cost: free

NASA's Space Place

NASA's Space Place

The Play section of NASA's Space Place web site includes "Unscramble the Clouds" and more.
Creators: NASA's Space Place
Price: free

PhET simulations

PhET (Physics Education Technology)

PhET is large collection of simulations and virtual labs covering a range of scientific disciplines and mathematics. The original focus was physics for college students, but the project has expanded into chemistry, biology, and Earth science. Many of the sims are suitable for K-12 audiences.

Partial list of PhET simulations covering atmospheric science topics: Balloons & Buoyancy, Glaciers, Gas Properties, Greenhouse Effect, Molecules and Light, States of Matter: Basics, Bending Light, States of Matter, Molecular Polarity, Reactions & Rates, pH Scale, Plinko Probability and Density
Creator: University of Colorado at Boulder
Cost: free

Smithsonian Science Education Center - Game Center - Weather Lab & Disaster Detector

Smithsonian: Weather Lab & Disaster Detector

The Game Center section of the Smithsonian Science Education Center includes Weather Lab, a simulation/app, and a game called Disaster Detector. Disaster Detector has tornadoes and hurricanes among its disaster types. Weather Lab explores large-scale weather patterns across North America.
Creators: FableVision (Weather Lab) and Filament Games (Disaster Detector) for the Smithsonian Science Education Center
Cost: free

Toy Models of Climate System from CSU

Toy Models of Climate Systems

Several (20+) "toy" models representing various components of the climate system, the carbon cycle, and land-atmosphere interactions. Developed using the R programming language and primarily intended for college students (though some are very accessible to high school or younger audiences).
Creators: Professor Scott Denning, Department of Atmospheric Science, Colorado State University
Cost: free

Weather and Climate Simulations from CIMSS

Weather & Climate Simulations from CIMSS

Several (17 as of November 2013) weather, climate, and atmosphere simulations and virtual labs.
Creators: Cooperative Institute for Meteorological Satellite Studies (CIMSS) at the Space Science and Engineering Center (SSEC) at the University of Wisconsin-Madison.
Cost: free

WeatherWise

WeatherWise (WXWISE)

WeatherWise is a large collection of simulations and virtual labs covering weather-related topics. Categories include: storms, temperature, humidity, precipitation, wind, clouds, radiation, climate, basic meteorology, and miscellaneous and non-meteorology. Some simulations are Java-based; others are HTML5.
Creators: Steve Ackerman and Tom Whittaker
Cost: free

Climate Simulations from the Concord Consortium

What Is the Future of Earth's Climate?

A series of five lesson modules with several embedded simulations. Includes "Earth's changing climates", "Interactions within the atmosphere", "Sources, sinks, and feedbacks", "Feedbacks of ice and clouds" and "Using models to make predictions".
Creators: The Concord Consortium
Cost: free