We have been to WDW many times in September, and the crowds are very low compared to the summer. If you have only been during the summer before, you will be amazed at the difference. Weather is an issue, but we have never had any of our September trips impacted by hurricanes or other weather considerations. We may have been very lucky, because many hurricanes in recent years have affected others' plans (especially in 2004). There is typically high heat and humidity, but this is easily manageable with a little thinking ahead. Just make sure you drink lots of water and try to plan a mid-afternoon break for swimming or just some rest. In our opinion, the benefits of the low crowds in September vastly outweigh the risks associated with weather.
To answer the questions posed by nluvwithmickey: A "walk-on" line is just that - you walk through the queue without stopping and board the ride. This is fairly frequent during September, and we have encountered this on just about every ride in WDW at various times, depending on the time of day and the date in September when we were there. We also encountered many FP machines closed during September 2004 and September 2005 (particularly in 2004 when one of the hurricanes caused many cancellations and then moved to the west, leaving a virtually empty park with no weather problems at all). Typically on our September visits, the longest wait we encounter is about 15-20 minutes, but a wait this long is very rare. We tend to arrive at the EMH park at opening and hop to a different park in the afternoon, so if your plans differ you may experience slightly heavier crowds. Even if the late afternoon and evening, however, we usually experience very low crowds.
Having said all of that, we have noticed that the crowds in late September are starting to grow a little in recent years. This is probably associated with the marketing efforts to get more people to come during the Fall, such as free dining. Last year, we were there toward the end of September and into the beginning of October, which overlapped with the start of
MNSSHP and the Food & Wine Festival. We particularly noticed heavier crowds at the end of the month leading into October, but "heavier crowds" is still relative - the crowds were still much lower than most other times of the year. We also noticed more people in the restaurants, probably because of free dining.
In general, we find September to be a great time to go. If you arrive early at the parks, you should be able to do pretty much everything that you want at a leisurely pace in 1/2 day or less. Have a great time!
