The Chemical Education Digital Library is a great resource for chemistry.  The site has lesson resources, educational games, links, communities, tutorials, digital textbooks and more.  It's a great collection of resources that can be used by the teachers and students in class as part of lessons, or as reinforcement, or help. 

NSDL is the nation's online portal for education and research on learning in
Science, Technology, Engineering, and Mathematics.

1. educational family-oriented underwater adventure 

PhyFun is a collection of physics games that are free to play and download. They are physics based, and include  platform, equilibrium, construction, demolition, motion, stacking and puzzle games and much more.  The games are fun, and can be used to demonstrate and explore different physics concepts.

Interactive Biology is a website that has videos, quizzes, and study guides for biology. There are fee based and free resources on the site, including free downloads of biology presentations. 

Use this highly interactive game to help middle school students understand scientific processes. The topic explored is food safety, but the students navigate through many processes to establish a recommendation for hand-washing behavior.  Scientific  processes investigated include observation, developing hypotheses, developing testing of variables, experiment design, drawing conclusions, and making recommendations.  Links are available to national standards.

The CSI Web Adventures are great, educational activities for middle school and high school science students. The CSI Web Adventures are also useful for teaching a research and investigation process that can be useful in almost any content area in which students complete research assignments. The CSI Web Adventures teach students to pay attention to details and examine all of the available evidence before reaching a conclusion.  The web adventures are designed to teach students the process of forensic investigation and problem solving. There are three cases or levels to the CSI web adventures. Unlike a lot of educational games, the CSI Web Adventures are created with the highest quality graphics and navigational features.

Rice University has partnered with CBS, the American Academy of Forensic Sciences, and the National Science Foundation to produce educational web adventures based on the CSI television series. 

Science Museum.org offers sixteen free online science games for students . The games are designed to explore a variety of science concepts including energy, genetics, environmental science. Each game is accompanied by a set of links to support and complement the content that game addresses.  The online games are designed for students of elementary school age, but would be useful in middle school setting as well. Science Museum also offers lesson plans featuring hands-on science activities appropriate for all grades from elementary school into high school.

Animation movies and interactive tutorials on:  anatomy and physiology 1, anatomy and physiology 2, biology 1, animals, plants, ecology, microbiology, astronomy,  geology, and physics.

Get schooled with lesson plans in five subject areas, including Science, Math, Language Arts, Social Studies and Health/Physical Education. Uncover the fascinating world of water and explore the issues facing our planet’s most precious resource.

Cruise through a sampling of my favorite science activities aligned with the Illinois Learning Standards for Science (middle school level). The lessons have been created for use in my middle school classroom with the Prentice Hall science series. You will also find some great lessons submitted by other teachers.

Late Nite Labs provides online chemistry and biology laboratory simulations for high schools, colleges, universities, and distance learning. Currently used by tens of thousands of students and hundreds of institutions of learning and science education programs, the always-available REACTOR™ chemistry series and RADIANCE™ biology series of virtual labs supplement and enhance students’ grasp of lab concepts and techniques and contribute to science education while reducing costs for instruction providers.

The Encyclopedia of Earth, an electronic reference about the Earth, its natural environments, and their interaction with society. The Encyclopedia is a free, expert-reviewed collection of articles written by scholars, professionals, educators, and experts who collaborate and review each other's work. The articles are written in non-technical language and are useful to students, educators, scholars, professionals, as well as to the general public.

ViranoExplore a Virtual Volcano

ScienceScene is a site with some great resources for Physical Science and Environment Science classes.

There are links, useful software to use in the class, news, virtual museums, references and much more

 Livebinder of Physics Resources has resources, lesson materials and activities, links, and more, all organized by Physics units and topics.  It is well organized with some great resources including video clips from the Mythbusters and other fun resources, simulations, and virtual labs.  It is a great resource for teachers or students, especially for a beginning teacher looking for some help getting their lessons organized and finding resources

A fun online physics puzzle game.

All about dinosaurs.

The computer will randomly pick a term used in science. Discover the word the computer has picked by guessing which letters are in it. Each incorrect guess you make causes the atom man to decay. Solve the puzzle before the atom man completely decays!

A website to introduce elementary students to 37 different kids of produce -- many they may not know.  Journey to Asia, a walk in the woods, tree house weather kids and much more.

The bug investigators (Andybiotics) tells you about the good bugs and the bad bugs in your body.

Science teachers especially have plenty to love and appreciate with this valuable resource. Everything from microbiology to astrophysics makes an appearance through a channel operated by a museum, university, educator, professional or interested individual. Because so many of the sciences require visual aids to really open up and explain their very cores and valuable applications.