[python] Running an outside program (executable) in Python?

Your usage is correct. I bet that your external program, flow.exe, needs to be executed in its directory, because it accesses some external files stored there.

So you might try:

import sys, string, os, arcgisscripting
os.chdir('c:\\documents and settings\\flow_model')
os.system('"C:\\Documents and Settings\\flow_model\\flow.exe"')

(Beware of the double quotes inside the single quotes...)