Links not on the main list. Smaller or more esoteric projects, or things built in old tech like flash. Worth digging through.
If any links are broken, let me know.

CPU Balls

Relative Hell
Trippy game which takes place in a strange geometric world unlike our own. Two actually, one with de Sitter spacetime, and another with anti-de Sitter spacetime. Created by Zeno Rogue.

Clim’ City
Sim city style game about climate change. Currently only available in French, and also quite a bit out of date. But I love it. Created by Cap Sciences.

QPong
Confusing game about building a quantum circuit to play pong. Good luck! By kirais.

Simple Circuit Simulation
As the title says, a pretty basic, though visually interesting, simulation of an electric circuit. Helpful for understanding electron flow. Created by Electricity Explained.

Gravitee
Classic web game about playing golf in space, having to take the gravity of various objects into account. Created by Funky Pear.

Genetic Walkers
Evolving creatures walk better and better. Created by Rafael Matsunaga

Quantum TiqTaqToe
Tic Tac Toe with quantum mechanical rules, for both web and mobile. Created by Evert.

LabXchange Library
Wide variety of simulations and virtual labs, covering biology, chemistry, physics and more. Curated by LabXchange.

Particle Sandbox
A gravity simulator for the web. Created by apexearth.

Optical Microscopy Primer
Many, many pages explaining the history of microscopes and how they work. Occasionally has some interactive simulations mixed in. Created by Michael W. Davidson.

Logic Gates
Part game, part quiz about building logic gates. Created by Keremoner.

QUARKED! Adventures in the Subatomic Realm!
A full multimedia quark adventure, with videos, stories, and games. Created by a team led by Alice Bean.

goREACT
A periodic table where you can drag various elements around, and see which ones interact with which. Created by the Museum of Science and Industry in Chicago.

Evolution Simulator
Simulating evolution with little avocado-blobs running to get food. Built by MinuteLabs.

An Interactive Introduction to Fourier Transforms
An approachable look at Fourier Transforms. Or, what sound waves, cool circular drawings, and jpegs have in commmon. Created by Jez Swanson.

Bloch Sphere Simulator
If you’re looking to simulate the state of a qubit, and how quantum logic gates will affect that state, look no further! Created by saich08.

Star in a Box
Explore the Hertzsprung-Russell diagram and how stars of various sizes evolve. Built by Jon Yardley, Stuart Lowe, Edward Gomez, Haley Gomez, and Chris North.

Optika
A game that involves optics, aiming lasers and such, loosely based on physics. Created by PlayZilla.tk.

Immune Defense
Fight off diseases using microbiology. Created by Molecular Jig Games.

EMANIM
A tool for exploring and animating electromagnetic waves. Created by András Szilágyi.

MOLEK-SYNTEZ
A complicated puzzle game where you’re building large molecules. Created by Zachtronics.

Hard Chip
If you’re looking for a game where you design physical computer chips, this PC game is for you. Pretty complex. Created by Elorth.

Standing Waves
Simple simulation where you can control a wave. Built by Nerd Island Studio.

Spintronics
A digital simulator of Spintronics, a physical science toy that lets you build electrical circuits modeled not with wires and electricity, by physical analogs of spinning gears. Built by Upper Story.

Quantum 3 Game
Game for iPhone (Android version not working) where you basically play a match-3, but with quarks forming hadrons. Created by Michigan State University.

Airfoil
A long interactive blog post about how a wing works, simulating the movement of air and pressure. The post gets into lots of related physics along the way.

Relativity Simulator
Various simple, short simulations of Special Relativity. Created by Alex Reinhart.

Physics Simulations
Lots – hundreds at least – of small physics applets, around a wide range of topics, separated out into two semesters of college physics. Motion, thermo, EM, waves, and optics all covered. Created by Andrew Duffy.

Virtual Oscilloscope
Very simple online oscilloscope that you can fiddle the knobs and buttons on. Created by PhysicsZone.

Gravity Lab
Gravity simulation by the National Science & Tech Medals Foundation.

SPH Fluid Simulator
Simulation using SPH of a ball in water. Created by Hector Arellano.

Creatures Docking Station
An old (2001) virtual life sim where the creatures have digital dna and traits are passed down accordingly. Surprisingly complex. Created by Creature Labs.

Quantum Puzzle Generator
A mobile explanation/game about qubits and quantum gates. Created by Dimosthenis Michailidis.

Donkey Kong Country with Relativity
A platformer game that includes some relativistic effects. By the SyllabusGames YouTube channel, in association with this video: https://youtu.be/bHGTDTIE23c

Space Time Travel
Website that has tons of videos, simulations, and mathematical explanations of how to visualize relativity. Created by Ute Kraus and Corvin Zahn.

PBS Periodic Table
An interactive periodic table by PBS media, which includes a little mystery game to match elements to their descriptions.

Peppered Moth Game
Simple game about natural selection, with moths of different colors. Created by Craig Tevis.

SWC Physics Simulations
Collection of physics simulations, with many interactive graphs, created by H. K. Wilfred Lee.

Neutron Star in my City
Fun toy that shows what it would look like to have massive space objects floating over your town. Created by Daniel Wysocki and HanGyeol Suh.

Foldit
Fold proteins as best as you can. A classic ‘citizen science’ game where by playing you can help investigate the science of how proteins get their shapes.

Quantum Marble Maze
A very neat downloadable java game about quantum mechanics. Created by Crispin Cooper.

Sim Bucket
Various small simulations about chemistry and physics, created by Nerd Island Studios.

Quantum Chess
A variation of chess that includes some quantum rules. Created by Selim Akl and Ryan Kartavicius.

Spore
A game about evolving creatures, all the way to space if I’m not mistaken. Created by Maxis.

Eterna
Learn how RNA fits together by playing this game. Created by Nova Labs.

Visualizing a Black Hole
Simulates the path of light around a black hole, and you can drag your view around. Created by Antonell.

Gravitation Physical Visualization
Flash interactive that shows a visualization of the curvature of spacetime. Created by Adam Trepczynski.

Psi & Delta
Game exploring quantum mechanics where you’re a little robot traveling along a wavefunction. Created by folks at Georgia Tech.

Superposition Arcade
Game about quantum logic gates, where you use gates to direct falling balls. Build by rsoiffer.