fbrun is basically equivalent to the "Run..." dialog in other desktop environment. This means that it is an easy way to start a program that isn't contained in the menu (or needs a special set of parameters for this particular invocation).
Another way fbrun can be useful is to be called from the menu with a preloaded command line that you can edit and then execute. An example might be sshing to a very long host name with lots of options of which one changes all the time. In this case, you could add an entry for fbrun to your menu that contains all the options and the host name. When you use said entry, you could edit the line as necessary and execute it.
fbrun has various options:
-font [font name] Text font -title [title name] Set title -text [text] Text input -w [width] Window width in pixels -h [height] Window height in pixels -display [display string] Display name -pos [x] [y] Window position in pixels -fg [color name] Foreground text color -bg [color name] Background color -na Disable antialias -hf [history file] History file to load (default ~/.fluxbox/history) -help Show this help
Most of those options should be self-explanatory. The options -text and -hf maybe need some explanation. The former is used to specify the pre-loaded (editable) text inside the fbrun window. If you'd like to specify multiple arguments (like ssh -X -f), be sure to wrap them in quotes:
fbrun -text "ssh -X -f"
The -hf option specifies the history file, which is a place where fbrun keeps its "memory" of the command lines you used (just like bash does). Normally you don't need this option, then the default is used. It might prove useful if you have multiple fbrun entries in your menu and want to keep separate histories for each of them.