I am unable to run a java application inside my firewall which is ISA
server.  I know it has to do with authentication being passed to the
server but am unable to solve

are you trying to run the application on the firewall server?
Try this link
http://www.isaserver.org/tutorials/Troubleshooting_ISA_authentication_issues.html

No, I am trying to run the application on a computer behind the
firewall.  I also note that netscape won't run on any of my computers
behind the firewall, and I assume this is for the same reason.

did you install the firewall client on the computer running netscape?
do you have any protocols rules define?
can you access the internet from different computer?
make sure in netscape to put the proxy info: ISA server ip address, port 8080
and same for all the protocols.

did you install the firewall client on the computer running netscape?
YES
do you have any protocols rules define? YES, but only what came by
default
can you access the internet from different computer? YES and from this
one as long as I use Microsoft products
make sure in netscape to put the proxy info: ISA server ip address,
port 8080
and same for all the protocols. I have

The actual error message I see in the java console is this:
java.io.IOException: Unable to tunnel through proxy. Proxy returns
"HTTP/1.1 407 Proxy Authentication Required ( The ISA Server requires
authorization to fulfill the request. Access to the Web Proxy service
is denied.  )"

on the ISA Management Console Right click on the computer name, Hit Properties
Click on the tab (Outgoing Web Requests)
Click on the Server
Hit edit
click basic authentication, Select domain, enter your domain name.
hope it works
In short you need to enable Basic authentication