Presentation programs such as Microsoft PowerPoint or Apple Keynote make clever use of the secondary monitor in a dual display setting: For example, if you are using your notebook with a projector, the projector will show the slides, but the notebook will function as a kind of teleprompter, showing the slides plus additional information. This additional information can be notes, the current time, the remaining time (when you specify the maximum duration of a talk), the next slide, etc. This is obviously helps with time management and smooth transitions between slides.
And then there are those of us who use LaTeX to produce PDF files with their slides. I like the fact that I can have a pure PDF work flow (especially handy on Mac OS X with its native PDF support) and that LaTeX is cross-platform (I use Linux at work, Mac OS X at home). The latest TeX Live distributions already come with the Beamer Class which is easy to use, well-documented, and includes several themes. I have yet to discover a program that has as many features as PowerPoint or Keynote, but at least I have found two options for showing the notes in a PDF file on the secondary monitor: