A treasure trove of interesting questions and answers from Washington State University. With guidance, some of the illustrations and animations may be useful for middle school students. This site is going to be moved soon and the URL will change, but you will still be able to get to the new site by a link from the old site. Comprehensive if not encyclopedic source of information, plus activities, careers in neuroscience, etc. A great science museum in San Francisco.
Name says it all.
A long list of sites that you may want to sort through and pick the ones that would be useful to your students. Better yet, develop a rubric for judging websites and let your students do the work. Dictionaries, encyclopedias, almanacs, atlases. Science content is mostly text, not much in the graphics department, at least from my preliminary searches. Reading level seems appropriate for most middle school students.