Although empty values are allowed in the arrival_time and departure_time fields in the GTFS stop_times.txt file, these empty values pose challenges to analysis tools that rely on knowing the exact stop times for all stops.
I have created a little utility that will update your stop_times.txt file with estimated values for the blank times. Currently, it just uses a simple interpolation method, evenly distributing stops in time between time points. If people are interested in a more "accurate" estimate, I might try to do something more complex that considers the locations of the stops along the road network and uses drive time to estimate the stop times. I'm happy to discuss technical details here if anyone is interested.
Download the tool here: http://www.arcgis.com/home/item.html?id=040da6b55503489b90fa51eea6483932