Write a program that does something linguistic that is useful for you. For example, you might want to write a program that collects some bit of data for you for a paper for one of your other classes, your prelim, your dissertation. You might want to write a program that can collect some bit of linguistic data that you are just curious about.
You can also write a program that does some bit of theoretical modeling, e.g. phrase-structure rules, Optimality Theory, Minimalism, Distributed Morphology, whatever. This is a trickier domain through.