Hello..and thanks in advance for any and all help! 

I'm traditionally not a coder..so I apologize for my lack of knowledge up front :)

I've sucessfully added a Java Script pop-up to my salesforce.com page using custom links.  It first checks to see if the window is already open...and if not it opens the pop-up.

var newwindow;
function popUp(url, w, h, namn)
{
newwindow=window.open(url, namn, 'width='+ w +', height=' + h + ' resizable=no, scrollbars=auto, toolbars=no, location=no, directories=no, status=no, menubar=no, copyhistory=no');
if (window.focus) {newwindow.focus()}
}
javascript:popUp( 'url', w, h, 'name' )

What I need now is to pass salesforce.com variables to the java script above.  I want to have the script pass login/password information that can allow the application that's being opened to auto/login. 

The next question would be...whats the best way to secure this login information if I am able to get it passed.