First start by taking the webserver out of the equation. Write an application in your language of choice to do the serial port control of your LED display. Set it up so you can control the various LEDs in the same way you want the webserver to be able to control them.
Then, once you’ve got a stand-alone application controlling the LEDs, put an interface on that to allow it to be called externally. This could be as simple as making it a command-line executable which took input parameters. On a Win32 box you could put a DLL interface on it so it could be called by another app. On Linux/Unix, you can do the same thing with shared library files.
Next, using your webserver programming language of choice, write server-side code to call your LED control app. This can be any server-side language you choose (Java servlet, PHP, ASP, Perl, etc.) as long as your webserver supports it and it can make the appropriate calls to your LED controller.
Lastly, once you’ve got a server-side script doing what you want, put a nice HTML GUI on it to give the users the choices you want to provide.
All of that is very vague, but you have to make some decisions on languages and architectures before anyone can be more specific. Do you want to use a specific language? A specific webserver and server-side scripting language? Do you have experience with things like COM DLLs or Java RMIs, or would you prefer something simpler like a command-line interface to your controller?