From Gnash Project Wiki

This page is for ideas about supporting drawing over a transparent background. A movie with no SetBackgroundColor tag might trigger this behaviour, if supported.

References

• http://lists.freedesktop.org/pipermail/xorg/2005-October/010882.html - It seems xeyes uses the XShape extension (is it an extension?) for fully transparent background. Fully-transparent means that events are also sent to he underlying windows rather then to the transparent one (they go trough the holes). Only limit is alpha accuracy: 1 bit only (either transparent or opaque). Attached to the message is an example code, a proof of concept.
• http://www.gtk.org/api/2.6/gdk/gdk-Windows.html#gdk-window-shape-combine-mask - GDK interface to the XShape extension