Are you talking about simulation at [url=http://www.phy.ntnu.edu.tw/ntnujava/index.php?topic=35.0]Propagation of Electromagnetic Wave [/url]?
The above case only show EM waves in 1D.

Electromagnetic wave are represented with Efield/Bfield vectors.
IT might be too complicate to visualize if too many wave are presented at the same time (too many arrows)?
It is possible to use waveform to represent waves moving uniformed in 2D. 

It will also be too complicated to present all wave in 3D.

Do you have a better ideas to represent many waves in 3D? Could you draw a picture and upload as attached file so that I can understand  what you want to do. Waiting for your answer. ;)