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Keynote has no freehand annotation capability and PowerPoints slide annotation doesn't work very well. A possible way to improve this was suggested in the “Annotate Everything — the Screen Scribble App” thread.
When in presentation mode, a helper app could put a transparent window over everything that could be written on. Whatever is written on the window would be associated with the slide shown below it, and when the slide is changed the annotation window would be cleared for the next slide. Of course, when the slide show is shown again, the user could, if they want, use the helper app to show the annotations from the previous session.
AppleScript is definitely capable of determining which slide is showing in Keynote. I'm guessing it is possible in PowerPoint also. (Anyone care to post PowerPoint's AppleScript dictionary?) So this is definitely possible. There would a lot to learn and do in building the freehand writing functionality. Wacom has an example drawing app and there are a couple open source apps to look at.
Please post how you think this should work and any suggestions.