We always travel in September. Usually, it's the last week in September (so that we can see Haunted Mansion Holiday) but this year we're mixing it up a bit--we're traveling the third week instead.
In the past, crowds have been fairly light to moderate during the week. Of course, Fridays, Saturdays, and Sundays are much more crowded. In '02, the crowds were so light that we didn't use fastpasses, and lines were never longer than 20 minutes, except for the Haunted Mansion Holiday, which was the only thing we fastpassed. In '04, the crowds were heavier, and we did get to use the fastpasses, but crowds were still pleasantly light. I think that you make a trade-off--crowds are light, but a lot of rides are closed for refurbishment.
Hours are shorter--in '04 DL hours were 10-8 during the week, and DCA was 10-6.
Weather in '02 was a little chilly, with light drizzly fog on some of the days we were there. It did get warm enough to swim on a couple of days, but it was too chilly after dark to swim. In '04, I seem to recall that it was pleasant to a little too warm for us, but I like temperatures above 70 and below 80.

It was plenty warm enough to swim during the day, but a little chilly in the early mornings and evenings. I recall that getting completely soaked on Grizzly River Rapids didn't make us turn blue.
As another poster mentioned, the Matterhorn is closed at this time of year, but from what I can tell, it's every other year. It was open in September of 2003. I've never managed to be there when it's open, but this year is my year! Haunted Mansion closes around the beginning of September, and usually opens the first Friday in October.
For specific information on the parks, I like to go to mouseplanet.com and look at their park updates. The archives are listed by week on the left hand side of the screen, and you can look all the way back to Dec. 2002.