Yes, I'm asking for what language to use, and how to make it "tell" the Arduino what to do.
My "vote" is for the Processing
program, given the broadness of your query. Other forum uses suggested it, too, earlier in this thread. One thing may be confusing - Processing is Java based, and the Arduino is C++ based, so the languages are similar but there are quirks of syntax that drive me mad when writing in both IDEs for the same project.
With Processing you still have to write a program to use the pc mouse/keyboard/screen, and then you can use the same Serial-style library to send bytes with commands and parameters to the Arduino board. You still have to write an Arduino program to recieve and interpret the bytes and do what it needs to do to the pins (and the same with sending results the other way). There is a readymade program Firmata for the Arduino that makes it easier to control it from the Processing program (or any other program on th pc), but I have not tried it ior looked at it in detail.
EDIT: Just saw a good example at http://arduino.cc/forum/index.php/topic,50449.msg359623.html#msg359623(NB: This was my 100th post)