You could use Eclipse. Eclipse for Java is a state of the art ide, and from what I have heard so far, so is Eclipse for C/C++. Netbeans for C++ is also a viable choice, along with Code::Blocks.
As for the console, I do not know if you can do it. You are running a console application and you don't want it to appear on a console? What kind of sorcery is that? Ok you could maybe just download an interactive shell for windows or something and manage to achieve what you want.
As for the timer, IDEs such as Visual Studio (the paid editions, can't talk about express edition) and Eclipse or Netbeans, feature a profiler, either by default, or by an add-on you must install, which can be used to evaluate your program and run several metrics on it.