FlowJo gives you the most flexibility possible with exported graphics.  You can easily ungroup any graphic, and change the font attributes, line styles, etc., to make any graph look exactly the way you want!  The first page in this section gives you some additional hints on exporting graphs.

The greatest strength of FlowJo is its ability to represent batch analysis in a simple and flexible structure.  Don't expect to find a macro language or scripting extensions.  Our approach lies in the grouping structure, within the workspaces. Create your layout, and with a single button, produce a stack.  The stack can be shown as a new layout, a tiles picture or a movie.  There's even a section about how to cancel batch jobs once they've been started

Drag-and-Drop is an important skill to learn if you are going to be a fluent user of this program. This section talks about the semantics of what it means to drop gates or statistics onto populations.  A few modifier keys can save you all sorts of time.

Indeed, modifier keys, especially the option key are used heavily in FlowJo. Use option dragging to duplicate graphs in the layouts, or option-close to close all your windows at once.   Try depressing the option key as you browse through menu items; you will find that many of the menus change to be a different command, giving you quick access to even more powerful features.