public class Executer {
    public static void main(String [] args) throws java.io.IOException {
       Runtime runtime = Runtime.getRuntime();
       // note the escaped double-quotes
       runtime.exec("\"c:\\program files\\textpad 4\\textpad.exe\" new_document.txt");
       //            ^^                                         ^^
    }
}

String commandStr = "\"" + COMMAND + "\" " + options + " \"" + firstfile + "\" \"" + secondfile + "\"";
Process process = Runtime.getRuntime().exec(commandStr);
BufferedReader buffReader = new BufferedReader(new InputStreamReader(process.getInputStream()));
String line = buffReader.readLine();