Links to other collections of science interactives. Get ready to get lost in more lists.
If any links are broken, let me know. 
The Falstad Collection
Collection of small simulations created by Falstad.
Explorable Explanations
A collection of Explorable Explanations curated by Nicky Case.
oPhysics
A large set of interactive physics simulations built by Tom Walsh. Covers a wide range of physics, including forces, waves, and light.
Academo Collection
A collection of small open source physics simulations, created by Academo.
Ricky Reusser Collection
A lot of cool interactive math-y explorables to check out. Created by Ricky Reusser.
PBS Learning Media
Collection of various science learning resources hosted by PBS LearningMedia. Covers topics such as physics, biology, and geology.
Red Blob Games
A variety of interesting lessons, simulations, and explorables about topics in math, physics, and programming. Created by Amit Patel.
The Physics Classroom
Sets of pages with lessons and interactives about a variety of physics topics.
PhET
The definitive collection of free online resources for physics classes. Run by University of Colorado Boulder.
Concord Consortium List
A collection of science interactives by Concord Consortium.
Dan Schroeder Physics Educational Software
Physics education software created mostly by Dan Schroeder, some excellent simulations in here.
Fowler’s Physics Applets
Collection of small physics simulations, many including nice explanations. Built by Michael Fowler.
A Free Particle Interactives
A set of Desmos simulations covering a wide range of physics including many about mechanics – an excellent resource for teachers and students. Created by Michael Freeman.
ScienceGameCenter
THE definitive list of science games – both digital and physical. Curated by Dr. Melanie Stegman.
Tesseralis
Set of simulations and explorables about math, created by Nat Alison.
myPhysicsLab
Lots of small simulations of things like pendulums and springs, where you can easily change the values, too. By Erik Neumann.
Universe & More
A collection of interactive physics resources that are fun and easy to use. By Matthew Blackman.
Astro Apps
Collection of interesting astronomical and cosmological simulations, created by Haus der Astronomie.
Index of Simulations
A spreadsheet pulled together for teachers of a categorized list of hundreds (wait, thousands!) of simulations you can find online, sorted by topic. An incredible resource organized by Helen Reynolds.