Here's what I think:
The way of communication from the Java on the client depends entirely how you implement it in the app.
In any case you'll have to make a request to the server, along with POST data, or as you suggested just a GET request.
You could of course implement any other protocol, such as SOAP and have the PHP script act as a SOAP server.
The client side applet will have to establish a connection and talk to the PHP script that way.