I'd like to install some application in my website which build by joomla open source, but seems javascript will be ignored by joomla, I may be wrong..? but Any help would be highly appreciated

B.Rgds
Bahsis

Yep you will be wrong.

But not sure how anyone can help without actually know what the problem is!

I am just guessing... Are you familiar with client, server, header relationship?

If you want java script for joomla there are so many things which is really great. Because joomla is open source in all these there are so many things which is really great for these there are so many web sites are available.

Adding java script in Joomlla
<?php
$document = &JFactory::getDocument();
$document->addScript( '/media/system/js/sample.js' );
?>

I have the similar problem, could i add my chat room which is based on java to joomla? what should i do?

based on java

Java and javascript are two different things.