FlowPlot

I use this to plot my FACS data. You can group your data files for example wild-type and treated groups can be plotted side by side. You can then export in almost any format including .eps which can be opened in Adobe illustrator for labelling etc.

The current code plots the FL2-H channel (PI-stained nuclei). You can plot any channel you want by changing line 167 in this file:
    
[n, xout] = hist(data(:,4),200);

For example: use [n, xout] = hist(data(:,3),200); to plot data from the FL1-H channel.

Using the GUI, you can reorder the groups or files within them to change the order of plots.

Flow Cytometry Data Reader And Visualization inspired this file.

Updated the description with more details.