Tree structure of presentation
The idea is to allow not only vertical slides which themselves have linear structure, but also to allow them to branch. In other words, allow all slides to have children as well as siblings, which also may have children, etc. The natural way of traversing such slides is by doing a DFS traversal.
I like to use such "structured" presentations. To see what I mean, you can have a look at my presentation: http://www.mimuw.edu.pl/~szymtor/talks/Verification%20dresden.swf, best visible starting from slide nr 5 (I use my own plugin for creating those presentations, but I'd be very happy to move to slid.es).
Another related thing apparent in my presentation is that the tree structure is visible and is imitated by the movement of the viewpoint, and the zooming in and out (deeper nodes of the tree correspond to smaller slides). The hope is that this movement helps convey the structure of the presentation to the audience (it may also cause nausea if used too much). This is a bit similar to prezi, but with the difference that the zooming follows a tree structure.
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Max Rahder commented
I'd like a navigation/tree pane on the left too, synced with the slide being shown. It would show child items for those slides that navigate vertically. The question is what would be the text of the tree nodes? The first <h1> or <h2> found on a given slide?