It depends a little on when you are going in September. Labor Day is late this year (September 7th) and it's the traditional "end" of the summer season for the parks.
After Labor Day, the hours tend to be shorter (on weekday), with much of the nighttime entertainment (e.g., fireworks and F!) is limited to the weekends (Fri-Sun). No one knows what the schedule will be for Paint the Night (the new parade), but WoC will likely be daily (based on history). Historically, the last Friday in September is when the Mickey's Halloween Parties have started, which impact nighttime schedules. Last year, the dates were not announced until July.
Weekends in September tend to be busy because of HalloweenTime (which will probably start somewhere between September 12 and 18 - it has not yet been announced and probably won't be announced for a while). Weekday crowds are fairly manageable. Labor Day weekend (Sep 3 to 6) is when the
Disneyland Half Marathon is slated to occur. It also happens to be a three day weekend for some folks. So I would expect fairly high crowds for that weekend. Likewise, as
planningjollyholiday mentioned, September 18 is the Fall Dapper Day, so anticipate high crowds that weekend.
September is a fine time to go, especially if you like Halloween and wait until HalloweenTime starts. There is probably a narrow window between the end of "summer" and the start of Halloween, when crowds will be low but some things will be closed (e.g., Haunted Mansion, Space Mtn) to have the Halloween overlays installed. Once HalloweenTime starts, the weekends will be busy, but the weekdays are still (for the most part) okay. In terms of weather, I find September to be a variable month. It's mostly warm, but it can cool down in the evenings.
You can get a sense of the historic park hours and entertainment offerings by looking through the wdwinfo archive of park hours.
HydroGuy has a thread with direct links:
http://www.disboards.com/threads/historical-dlr-park-hours-entertainment-and-refurbs.2291124/
