KLDazey:
I do appreciate the Arduino environment, but when writing the program I am use to using those libraries as this is how I have been writing codes over the last few years. I just recently started using the Arduino.
I guess you do not quite understand why you (have to) include those files. If you don't use stuff from iostream, you do not have to include iostream.h; if you do not use windows specific stuff (e.g. write a console application), you don't have to include windows.h.