Build An Atom is a physics simulation tool by University of Colorado. This tool deals with the concepts of atoms and atomic structure. In a nutshell, it shows how different elements are made by adding or removing protons, neutrons, and electrons from atoms. The simulation was written in Java, so it can be run on Windows, Mac OS X, and Linux and it can also be run from a Java-capable web browser.
The simulation consists of a graphical representation of an atom. The nucleus holds protons and neutrons, and electrons orbit the nucleus. There are three buckets at the bottom of the screen. From there, you can drag each particle to the atom. Protons and neutrons will only remain inside the atom if you place them in the nucleus. When you start adding protons and neutrons, the name of the element you have created appears inside the nucleus. There is a table of periodic elements where you can consult all the elements. There are also two panes where you can see the mass and charge of your custom-built atom.
The simulation is very illustrative and there are good teaching and learning guides online that you can download for free.