It is depends on what you want to share and how it will be used.

The applet is good for web distribution, user only need a browser and most of the browser support java applet. The most import point is security, the applet would not be able to read or write to your computer without your permission.

User need to install Java RUN Time in order to run java as an application (Click jar file to active the program).
Java application can have [b]full access to the computer file system[/b] when it is running. (It means that java application can read and write to your computer just like ordinary executable files.
You will need to be careful if you have receive program from someone you do not know.

If your simulation also includes image or movie files, you need to add it to the jar file.
Click the image just under [u]close window[/u] picture at the top right corner of EJS window.
When you move mouse over that image, "[u]information about this simulation[/u]" message will show up.
Click the image and select files for the "Files required" field. This will tell EJS to include files you have selected to the jar file. So that user will be able to use it when it is running either as applet or application.