I don't know of a way to search for flights to anywhere at a particular time, it can probably be done with GDS access though.

There was a SFO-BOS which left at 12:06 (UA178?), but I think that has gone off the winter schedule. LAX-ORD also used to leave just after midnight, 12:09 or so, but that looks like it is back to 11:59pm now.