I have made a great deal of progress with R2C2 (RepRap Control Center). After a bit of hacking I was able to get the RepRap host software converted into an applet. The RepRap host software communicates with a couple platform depended libraries via Java Native Interface (JNI) for java3d (used to render the STL files in a 3d environment) and rxtx to communicate with the RepRap motherboard. In order for the currect RepRap host software to be easily converted into a web app, the applet utilizes Java Network Launching Protocol (JNLP), which allows the neccary platform dependent libraries to be loaded onto the client computer.
The next step is to split the RepRap source into a client/server model. Most of the classes in RepRap gui package will be added to the client package while all classes interfacing with the RepRap motherboard will be added to the server package.