You mentioned PhP, but do you also require that they run it thru a web interface? I mean, if they are commandline programs, would a simple GUI (Graphical User Interface) be ok, so they could run the program on their own computers? If so, you have a wide choice of GUI toolkits to choose from.

There is Tk, Tkx, Gtk2, and Wx just for starters. You could write simple little programs that let the non-geeks click on a button to run some CLI of yours. It would be alot easier than dealing with all the permissions problems that a web based program will present.

I'm just mentioning it. Do the non-geeks have the need to run the program from anywhere on the internet? If not, why expose your CLI program to the world?