You could try a top-down approach: code the overall logic first, with the details simplified into function calls, and then go back later and write the functions (which can themselves contain function calls, to functions that you can write later...).

Yeah, I know, that's not all visual and graphical and multimedia and cool and stuff. Nonetheless, it works reasonably well for most purposes.

See my answer on the Beginners Perl mailing list.

Agreeing with the above that it's entirely independent of language used anyway, I figured I'd mention Dia for doing charts and whatnot. Maybe this is in the right direction.

There are basically two kinds of flow charts: One describes an algorithm (instead of using pseudo code; a good example is here, the other gives a high-level overview over how different components interact in a complex application.

As has been pointed out, both are language independent.

And the second one is usually a lie.

Most complex programs these days are object oriented, and that means that that whenever you obtain data from an object outside your own class/package/module, you call a method from another class or object. So a real-world application crosses the border between classes thousands of times, instead of having a smooth border that is crossed once or twice.

Instead of showing the control flow, it would be far more interesting to know what objects are shared between subsystems, or through which objects subsystems interact with each other.

Which brings me to my main point: For a complex system, a detailed flow chart is usually too complicated to show anything of interest, and a simplified flow chart is usually a lie and often not helpful either.

So if your program is getting so complex that you lose overview over the control flow, it might very well be a sign that you could use a better approach. Like objects which don't care very much about control flow, because they are well encapsulated.

I never used a program to do it, just a large dry erase board, a marker, and some larger sized post-its.

Its simple to use and takes almost no time at all to get started. I can move things around quickly, draw/redraw lines between notes, stack notes on top of other ones, or replace notes all together.

I think if I had used some kind of visio-type program I would have spent all my time playing with different boxes/borders/fonts/colors or at least spent time learning the ins and outs of the software itself when what I really wanted was to get to work solving the problem at hand.