I recently came across this great free (but not FOSS) flash visualization application http://www.sacmeq.org/statplanet.
There is an Excel “Data Converter” to ease the loading of data, under GPL. StatPlanet itself is not open source, though free to distribute. It includes nice maps a GapMinder-type bubble chart, and can be run offline, in contrast to Google Motion Charts.
I think it should be quite feasible to generate the “data.csv” input files, so that desktop users of DHIS can use this nice tool to analyze and play with their data once entered in DHIS 2. (It does however not seem to have multiple GIS layers, so I suppose only one OrgUnit level can be used at a time). A question would be how to manage various layers, if needed.
Another issue is converting boundaries into flash - this seems a bit cumbersome, but is of course not something that needs to be done very often: http://www.sacmeq.org/statplanet/custom-map.htm#conversion
All in all, I think being able to output to the required format could be a big selling point for DHIS 2.