I'll add a formal comparison later, but for now I found it useful to list out some of Drupal's charting/graphing/data visualization options.
http://drupal.org/project/chart Google chart API
http://drupal.org/project/charts Charts
http://drupal.org/project/charts_graphs Charts and Graphs (D6)
http://drupal.org/project/csvchart CSV Chart (D5)
http://drupal.org/project/graphapi Graph API
http://drupal.org/project/views_charts Views Charts (D6)
http://drupal.org/project/views_sparkline Views Sparkline (abandoned?)
http://drupal.org/project/visualize Visualize (D6)
Integration with third party chart software
http://drupal.org/project/highcharts works with HighcCharts Library
http://drupal.org/project/flot Flot
http://drupal.org/project/fusioncharts FusionCharts
http://drupal.org/project/views_jsgantt jsGantt View
http://drupal.org/project/jsxgraph jsxGraph
http://drupal.org/project/open_flash_chart_api Open Flash Chart API
http://drupal.org/project/rgraph RGraph
http://drupal.org/project/swfcharts SWF Charts
See also
http://drupal.org/project/exhibit Exhibit
http://drupal.org/project/gvs Google Visualization API
http://drupal.org/project/drawing Drawing API
http://drupal.org/project/raphael Raphaël
http://drupal.org/project/graph Graph (abandoned?)
http://drupal.org/project/graphstat Graphstat (abandoned?)
http://drupal.org/project/graphviz_filter Graphviz
http://drupal.org/project/graphviz_noderef graphviz NodeReference
http://drupal.org/project/graphmind Graphmind
http://drupal.org/project/hypergraph Hypergraph
Deprecated
http://drupal.org/project/ofc_api Open Flash Chart 2 API