“The WMODE parameter can be ‘window’ (default), ‘opaque’, or ‘transparent’. Using a WMODE value of ‘opaque’ or ‘transparent’ will prevent a Flash movie from playing in the topmost layer and allow you to adjust the layering of the movie within other layers of the HTML document.” – Adobe Technote

In my testing this works great in Firefox 3 and IE 7.

Since we use FusionCharts at $work I had to figure out how to make the fusioncharts javascript set WMODE. This is very easy by calling a method on the chart object. Make sure you do this before you render the graph.

A thread on the fusion charts forums goes in to more detail about this.

Edit: Turns out that if you set a fusionchart to use wmode transparent or opaque, all of the mouseover events don’t work, such as displaying the exact value of a point in the chart when the mouse goes over it. Boo!