import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;

import javax.servlet.ServletException;
import javax.servlet.http.HttpServlet;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;


public class MapMime4Application extends HttpServlet {
    protected void service(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException {
        String path = request.getServletPath();
        path = this.getServletContext().getRealPath(path);
        File file = new File(path);
        if (!file.exists()){
            response.setStatus(404);
            return;
        }
        response.setContentType("application/x-ms-application");
        FileInputStream stream = null;
        try {
            stream = new FileInputStream(file);
            byte[] buf = new byte[(int) file.length()];
            stream.read(buf);
            response.getOutputStream().write(buf);
        } finally{
            if(stream != null) {
                try {
                    stream.close();
                } catch (Exception e) {
                }                
            }
        }        
    }
}

修改web.xml, 增加：

   <servlet>
      <servlet-name>MapMime4Application</servlet-name>
      <servlet-class>MapMime4Application</servlet-class>
    </servlet>
  <servlet-mapping>

    <servlet-name>MapMime4Application</servlet-name>
    <url-pattern>*.application</url-pattern>
  </servlet-mapping>

修改后ClickOnce可以正常安装执行 :)