Your app will probably communicate with the Arduino via serial. How that will work depends on what programming language you decide to write your windows app with.
More recently I have been making my GUIs so they are viewed in a browser. I find it much easier to create screens with HTML and CSS. I use the Python Bottle web framework to create the server that produces the GUI stuff and works with Python code to talk to the Arduino.
Having done a little bit of web design long long ago, i have to ask if you ever run into browser compatibility issues.
Just found it impossible to work with TKinter.
Really? I've only done one thing with it, but I was surprised at how easily it went together...
I would recommend the language called Processing to write your code in. It is Java like which means it has the familiar C syntax.