I've moved on from some of my original flow mapping work of 2008/09 and am now working on different kinds of things. However, I came across some interesting work on geovisualisation at The University of Manchester Geospatial blog which made me want to revisit previous work.
In particular, the reference to a short population density animation caught my attention.
In short, I have experimented with 3D animated geovisualisations - in this instance it is of my London flow surface and flow lines using commuting data. There's a short video below (it may take a moment or two to load - it's a large file).