Flotec: the program was designed in a java language known as processing. it can be downloaded here: http://processing.org/
you are correct. it is run separate from the arduino terminal. if you want to interface your arduino sketch with this program, use the comm code in sample arduino sketch, included in the download.
general: I made a mistake. in an effort to clean the code a little before sending it out, I wound up crippling the program. whoops. many of you have already figured this out I'm sure, but AxisFont & TitleFont, while being declared in the correct place, cannot be initialized there. the initialization has to occur in void setup().
a fixed version has been put up here: http://arduino-pid-library.googlecode.com/files/PID_FrondEnd_v02-fixed.zip
sorry for the mess-up.
Brett