I also break my talk into logical chunks - say five or six sections. I practice each of those individually, timing them. This gives me an average for how long each section takes, so I have a schedule written down. This lets me know how far over or under my time allotment I am so that I can adjust on the fly, either adding some additional explanation to some areas or subtly truncating something.
I always know my "bail out" slide - if I end up running out of time, what's the "thank you!" slide number? If you simply type in that slide number in PowerPoint or Keynote, it will jump to that slide without fanfare. Don't ever tell your audience that you ran out of time to get to all your material, or flip through the slides to the end that they won't get to see. They'll feel like they were ripped off. (Also, make sure to structure your talk so that the special bonus material is at the end, so they're _not_ actually ripped off.)