Hey,
I think I understand what you're trying to do, but I can't say i've tried to control the board through a web interface.
I believe the webserver on uClinux distribution is boa: www.boa.org.
And I believe you should be able to write a CGI script to control the board.
However I am not sure how to access the LEDs from linux.
For an application like this, that is for controlling the board and for getting input from the board, I would take a different approach. First, I would write a server application that runs on the board and listens to UDP or TCP connections on a specific port. Then I would create a java applet on the PC to talk to the board. Then I would host that applet on the board, so that when you connect to it, the applet runs automatically.
This way, you can have more control over what you can do as opposed to the simple web interface. Maybe I can throw together a small demo of this approach, if anyone's interested.
-Thomas