Sorry, I should have explained... Touringplans.com, the website for the Unofficial Guide to WDW, has a crowd calendar where they predict the park crowd levels on a 1-10 scale w/10 being most crowded. It's based around the Magic Kingdom somehow. They also tell you which parks to hit on which days.
I can't really say about the weather since I think when we were there in May it rained a LOT more than usual. In Sept it usually rains every day but I think it gets better the closer to Oct, I'll find out for sure when we go. Personally, I would take heat over crowds ANYTIME!!!!! As far as the rain, it really didn't stop us in May. In fact, it kept the crowds down which was fine by me! In September, the rain doesn't last too long(unless it's a hurricane or something). My preference is fall I think, just because I love the decorations and Halloween party.
Here's Disney's crowd level info from allears.net:
The Lowest Attendance --
* January (except New Year's Day) until just prior to Presidents' Week in February
* The week following Labor Day until the week prior to Thanksgiving
* The week following Thanksgiving until mid-December
More Moderate Attendance:
* After Presidents' week in February through early March
* Late April through early June (except Memorial Day weekend)
* Columbus Day Weekend (October)
* The first part of Thanksgiving week
Highest Attendance:
* Presidents' week in February
* Mid March through Late April ("Spring Break")
* Memorial Day weekend
* Mid June through Labor Day
* Thanksgiving Day and weekend
* Christmas week through New Year's Day
Hope this helps!! Happy Planning.