You can’t control Java applications directly using windows. However, you can use JAB (Java Accessibility Bridge) provided by Sun Microsystems to inspect Java application.
You can download tools from Sun Website. Click the link below
Thin client is buzz word and often, major players use Java applet to achieve the same. If you still want your softphone to be installed locally and integrate with customer applications, I prefer to do this in this way.
If you have any other solutions, please feel free to let us know.