Mozilla preferences are stored in a .mozilla directory for each user, in their home directory. Thanks to Dr. Li, that I could find this out. Now if you run a program that uses SWT Browser, you can see a a folder "Eclipse" inside this .mozilla directory.
[Note I am talking about running a Java Program which has SWT Browser, from ECLIPSE, thus the folder name is eclipse. If you run from console, you might have a different foldername(I guess as that of the program name)]
It is in the /home/
Close Eclipse and start again. Now when you launch the program, the browser would use this preference.
Another way is to use "about:config" within your program do the configuration!
For this you can just write a configure() function and use it when you want. The function can be something like
public void configure()
Display display = new Display();
Shell shell = new Shell(display);
Browser browser = new Browser(shell,SWT.CENTER);
Now you can create new instance of ConfigurationWindow and call configure() which shows the user preferences window, just like the one you get when you type about:config in Mozilla Firefox.
This way one can configure preferences for Swt Browser Widget!