All sites are middle school appropriate. Elementary sites are grouped below.
Reading / Language Arts
Health
http://www.playnormous.com/games/brain-gain Test your brain with this online web game that's all about health! In Brain Gain.
Math
CoolMath.com has many games and tutorials, but it's easy for the kids to get focussed on only strategy games and only play puzzles instead of working those math skills.PurpleMath.com Helping students gain understanding and self-confidence in algebra.
Hoodamath.com
Math Playground Math Playground is an action-packed site for elementary and middle school students. Play a math game, solve a logic puzzle, and have some fun!
Multi-subject:
BrainPopJr.com BrainPOP creates animated, curriculum-based content that engages students, supports educators, and bolsters achievement.SheppardSoftware.com has activities from Pre-K to Middle School, in all subject areas. Excellent resource, my top recommendation for an educational website. Works great on a SmartBoard or IWB too.
FreeRice.com not only quizzes kids with increasing difficult questions, but even has classic art work identification.
Keyboarding/Discussion
http://todaysmeet.com/Elementary Level Educational Sites:
http://www.cookie.com/
Starfall.com Our systematic phonics approach, in conjunction with phonemic awareness practice, is perfect for preschool, kindergarten, first grade, second grade, special education, homeschool, and English language development (ELD, ELL, ESL). Starfall is an educational alternative to other entertainment choices for children.
ABCFastPhonics.com A different approach to phonics. ALL ONLINE -- ALL FREE