Sach writes...

Sach, somewhere in Australasia, wrote:

http://research.stowers-institute.org/efg/ScientificSoftware/Utility/FCSExtract/index.htm
 
Earl wrote a small macro to extract FCS binary to ASCii for the purpose of doing further analysis on R. Might be a useful resource.

For those of you without access to FlowJo, this would be a good alternative.