I have, yes. Think of it, in some ways, as an open-ended dungeon crawl. They have certain places they can go to start with, which influence later possibilities - just like choosing the left or right hallway.
The difference, of course, is that the PCs can wander right off the map much more easily. And usually do. My flow charts tend to have arrows pointing right off the page around the edges with notes that say stuff like "well, your adventure's screwed - improvise" or "not an ideal outcome - mass panic ensues"...
As a general rule, I usually try to plot out, not what the heroes are doing, but what the villians are doing, and who that will effect, and then let the events take their course. If the PC's discover what's going on, great! If not... well, bad juju happens. but that's the way it works.
The advantage, I find, in thinking of it that way is that it adds an aura of urgency and believability to events - they progress naturally, rather than waiting on the heroes to get to point A so event B can happen just a little too late.
If you're a mac user, I highly recommend Omni-Graffle for flowcharting.
jtb