We have been in June, Sept., Oct, Nov., Dec and Jan. By far Sept. was the lowest crowds. We have been to WDW 3 of the 4 weeks in Sept. with Labor Day week being the only one we haven't done. "Late" Sept. crowds are a little higher than the 2nd and 3rd weeks of Sept. but still very manageable. You may run into some 3/4 crowds when the crowd calendars say 1/2 crowd levels but even the 3/4 crowd levels in Sept aren't the same as 3/4 in June, Oct, Nov. or Dec.
I know that last sentence seems a little odd. Even with the "higher" crowd levels they are still low. This is one reason we plan most of our trips for the 3rd or 4th week in Sept. We know the crowds will be in our favor even when it is "busy".
For example: a 3/4 crowd level in Sept. there was a 45-60 minutes wait for Soarin. A 3/4 crowd level in Nov. the wait was over 90 minutes. Same crowd level but lower wait times. I'm not entirely sure how it works but that is what we have run into on a majority of our trips (almost all taken in Sept.).