For FlowJo v9:
-copy from the layout, then in ppt2011 choose paste-special (ctrl-command-v).
If you are missing the y-axis label on the graph, this means you pasted instead of doing the paste-special thing. I guess ppt2011 thinks FlowJo graphs are special. If you still have ppt2004, normal paste will do just fine, and one can even right click on the pasted graph and ungroup. Later versions of ppt removed this nifty feature.
If you have dotted (or otherwise non-solid line) histogram plots, make sure to uncheck the FlowJo Output Preference for "Copy histograms as polygons". Otherwise the pasted image will only have solid lines.
For FlowJo v7.6.4 (our current Java version):
-save the FlowJo layout with a filename that ends with ".emf" (layout1.emf), then in ppt choose "Insert Picture from File" to get a nice high resolution graphic from FlowJo into ppt. The default file format can be set in the File Format Preference.