The HTML5 simulations are the best place to start - they should work on all modern browsers and mobile devices. This collection (mainly aimed at introductory physics) currently has over 200 simulations.
The remaining collections are mostly Java simulations - those were getting very difficult to run, but now it turns out, thanks to Bob Hanson and Wolfgang Christian, the Physlet simulations can be made to work again by making them Javascript compatible.
There are three main collections of Physlets. Each collection can be viewed via the menu at left. The collections cover Physlets used in a typical first-semester introductory physics class, Physlets used in a typical second-semester introductory physics class, as well as our collection of prelab assignments that use Physlets.
As of today (Sept. 27, 2019), all the simulations in the "Physlets in the First Semester" collection AND the ones in the "Physlets in the Second Semester" collection should run. The pre-lab collection is still being worked on, so those have so far only been partially revived. The goal is for everything to be done by mid-October, 2019.
There are also some good simulations in the collection based on the Ejs (Easy Java Simulations) package from Francisco Esquembre.
The simulations and animations were scripted by Andrew Duffy at Boston University. Please direct any questions or comments to aduffy@bu.edu
The Physlet simulations and animations found here are based on Physlets from Davidson College. Have a look at the Physlet page on ComPADRE to see all the wonderful things you can do with Physlets.
The Ejs (Easy Java simulations) are based on the Easy Java Simulations package created by Francisco Esquembre.