What library/libraries do I need to add in order to communicate with an Arduino from my desktop Visual C++ application? At this point, all I really want to do is make an LED flash (write high/low to a pin). I already have the desktop application going, but would like it to interact with the Arduino. No, Arduino Uno is not suitable for my case.
Edit 1 Also: I am using a serial USB COM port to connect to the Arduino.
Edit 2 While I am programming in Windows, the application will be designed for Windows or Android.
In the Arduino side, you can just use the built-in Serial to send and receive data.
In the desktop side, refer to this question, which tells you how you can talk to Serial ports in Visual C++
EDIT:
If you are planning to use Java, then you can use the Java Serial port library without any changes to the Arduino code.
Also I would recommend you to use the Android APIs if you want to create an Android app. Using NDK is a real pain and unless you know what you are doing, it will be very tough.