I believe the one thing they for sure would close down is the Haunted Mansion for the Halloween/Christmas season. Crowds will be a whole lot thinner than the summer season since school is already in session. The upside to going on a weekend is that they show Fantasmic!
My family and I went in Sept 2005, the crowds were very bearable. I had previously only gone during summer while I was a child. My parents took my daughter to Fantasyland and my (now ex) husband and I strolled the parks alone. Our longest wait must have been 45 minutes, if that. We did take advantage of fastpasses. Fantasyland, I think my mom and daughter may have waited an hour or a little longer for Dumbo but small world and other rides prob under 45minutes. The wait did not seem to bother either of them and my dad told me that they were able to ride small world about 7-8 times (and all this and some other rides before lunch I believe). I love going in Sept for this exact reason. My daughter is not in school (well she just started today, pre-school) and while the parks close early and parades and fantasmic are limited, the time in the parks seem much more enjoyable to us. We're going again Sept 22-27th. (Note in Sept 05 we were there prob Sept 10-17th). For fireworks on the weekend we were able to show up 30 minutes before the fireworks and got seats in a roped off area at the hub (but more towards the maingate then the castle and we didn't squeeze in or ask people to scoot, there was just enough room there).
sept 05 we stayed at carousel, got it for 60/nt on travelocity. The room was good enough, the fridge was a good size. the only problem i had here was that on our last morning our sink backed up with dirty water, we ended up throwing whatevers towels we had on the floor to keep it from getting to our things. we called front desk 3 times and no one ever came within the last hour we were in our room. when we checked out we explained to them that unless they wanted water to start flooding the entire room they should get someone there to do something quick, it overflowed while we were still in there and tried to get someone to come but they never did while we were there. they also gave us wrong directions when we asked them how to get to a trader joes (the next trip we took i mapquested it and now i can do the drive without a map). because of the wrong directions and their lack of concern (and no apology about the overflowing sink) i won't book a room there again. Cheap no doubt and comfortable enough for 4 adults and my toddler. breakfast was free, fruits (apples oranges and bananas i believe) and pastries. coffee and juice, standard continental fare.
Mar 06 stayed at Hojos (110/nt, last minute reservations and this was a pretty good rate for the time). room was quite roomy but the walk was just TOO far for us after a long day at disney. Didn't find the check in to be as friendly as most other people will report so nothing special to draw us back here again. the fridge was smaller than that at carousel.
Nov 06 stayed at park vue inn (i think we paid about 70/nt or so, maybe 90/nt?). I would come back here, location location location. the room was similar to that of carousel (minus the over flowing sink) and the fridge the same size. continental breakfast similar to that of carousel. the free breakfast isnt really a factor for us as I love to go to mimi's for breakfast anyways (well those days that we dont go to goofy's or PCH grill). after a long day of disney even this walk seems long which makes me wonder how i ever managed to do carousel and hojos.
sept 07 was planning on staying at best western park place inn, switched to desert inn and now we're one night at paradise pier and 4 nights at GCH (because of the annual pass rates, originally had 189 concierge at pp but i wanted gch cause it is closer). bwppi we had a 1bedroom suite for 120/nt. desert in we had a room for 87/nt and now we're at pp concierge 169/nt and gch 199/nt. might as well try it when the rates are lower than it usually is.