Here are the most useful resources I've found and used in my years teaching middle school science. I've sorted them by science type but some may be used for multiple.
Big History Project - I haven't used it but our high school team is pretty stoked on it.
HHMI - EarthViewer - Cool simulation, they also have a ton of free resources they'll send you for free.
Scale of the Universe 2 - One of my favorite visuals for how big or small we are.
Solar System Scope - Awesome Solar System simulator with real time orbits.
Earth Nullschool - Really cool, current wind/weather/pollution viewer (with tons of other features)
Nova - Hunting the Elements - Great video when I get into atoms/molecules (you can find it on YouTube as well.
Periodic Table - Pretty awesome chart organizing the table of elements in all sorts of ways
MolView - Molecule viewer and creator.
Switch Energy Project - Awesome resources and documentary on alternate energy sources.
Chrome Music Lab - 13 different mini-apps that show off everything from sound waves, to music creating apps. Includes a spectrogram that can use your mic to show frequencies.
PhET Simulations - Tons of simulations with lessons to go with them (a bit hit and miss but the simulations are solid)
Gizmos - Like PhET simulations but not free.
LabCamera - Chromebook app with a lot of science related features. Free for teachers but not students.
NGSS Standards from NGSS - Better view of the NGSS standards with lessons and labs for each one.
CK-12 - Free curriculum you can use and customize.