As a result of my playing with mootools and creating powerpoint-style slideshows on webpages from restructured text, I am pretty much decided about turning this into a standalone, real application.
I am doing a PyQt4 frontend, and restructured text addons to generate the slides.
The native file format is restructured text itself, and it supports basic transitions between slides.
It still needs a ton of work, but here is a video showing how it looks after a couple of days hacking. You can see the current UI, a document's source, and a demonstration using firefox (only because Konqy doesn't suppose opacity, the rest of the transitions work even better on Konqueror)