Hydrogen Atom Orbital
Simulation code by java@falstad.com
Molecular Vibration
Images from Wikipedia 
Harmonic Oscillator
Simulation code by University of Colorado Boulder
Harmonic Oscillator (simplified)
Simulation code by Daniel V. Schroeder, Physics Dept., Weber State University
1D and 3D Particle in a Box
This simulation for PIB is not the greatest one that I found. Additionally, the simulation lags a lot. Thus, after inputing the dimensions of the box and the energy level, I recommend waiting a couple of seconds to see the output change.
Code by Cassy Chen, Rasmi Davu, Isabelle Zelaya (2018),"Particles in 1D and 3D Boxes"
2D Particle in a Box
Desmos template created by Dr. Powers-Riggs
Hydrogen Atom Radial Wavefunctions
Hydrogen Atom Angular Wavefunctions
Spin States
Feel free to explore the "Coins" and "Photons" simulations, but the "Spin" and "Bloch Sphere" are helpful simulations for visualizing the different electron spin states.
Simulation provided by PhET