We have been 5 times in September, going back again in a little over 2 weeks.
Weather - As everyone has said it's still hot, you get the occasional mid afternoon shower (but it's not everyday) and it is humid. One thing you should know, September is the peak of the Hurricane season in Florida.
Crowds - Quiet, 10-20 mins queue times for most things, the major attractions are generally up to an hour (it was quieter a few years ago but tourism is definately increasing). The first Monday in September is a US holiday (Labor Day) and can be a little busier, also there is Night of Joy at the Magic Kingdom the following weekend which can affect crowd levels. The other thing to bare in mind is the free dining which usually occurs in September, this fills all the table service restaurants making walk up's just about impossible to get.
Good Time / Bad Time - I would say it's a good time to go, the days are not too long (generally all the parks have closed by 9pm) it's quiet and the weather is nice. If you want to eat in the table service restaurants Advance Dining Reservations are essential.