This is a pretty straightforward question that you must answer HONESTLY! To prepare for this kind of question, brainstrom all of the differently programs you learned how to use during your high school and college education or any programs you may have used in previous jobs. Obvious examples are Microsoft programs such as Word or Works, Powerpoint, Excel spreadsheet, or other programs you would have used to create your homework assignments. Think about computer application classes you took: Did you learn how to create a Web page or take a Web design class? Which program did you use? Did you write for the school newspaper or yearbook or literary magazine? Which programs were used for those types of publications? Did you use programs specifically related to math applications? Did you take a digital photography class? Did you take an accounting class or other business class where you learned business applications? Your employer may want experience in a specific program, or may just be looking for computer skills in general.
This would surely depend to a huge extent on what sort of a job you are applying for. If you were applying for a teaching position, for example, you would want to talk about PowerPoint. If you were applying for a job as a secretary, for example, PowerPoint would be much less useful and you would have to discuss your familiarity with programs like Microsoft Word and Outlook.
If this is a generic question such as one for a school senior project (where you don't have a job in mind), you should simply talk about whatever software applications you have used that could possibly be useful for any sort of job at all. I would imagine that the Microsoft Office programs would be your starting point and then you could branch out into anything else (like graphics programs or Photoshop) that might possibly be relevant.