I used this to open ffmpeg in processing, it's a java fonction, this can perhaps help you. I don't know if it's only to open .exe or other things.

import java.io.*;

try{
             Runtime runtime = Runtime.getRuntime();
             Process proc = runtime.exec(
               "C:/Users/WhereArt/ffmpeg.exe" );//dos command
           }catch(Exception e){
             print(e);
           }