When are best rates in the fall?

Depends on where you are going. Also, there is fall vacation at various time in Germany, so I imagine Austria and Switzerland have one too. Check the vacation times at this website and check airfares. Usually prices drop fairly soon after summer vacation gets over with.
http://www.holidays-info.com/School-Holidays-Germany/2009/school-holidays_2009.html

Will fly into Frankfurt (hopefully direct with Lufthansa again)- not as worried about the lodging prices as the flights. With lodging there is much more room for creativity!

Hi, Cate. Oktoberfest in Munich definitely has it's ripple (Sept 19th - Oct 4th) on housing and airfare. Official government statistics show 6.5 million people attend, and 9% of them are staying in the surrounding countryside at some point, so lots of competition. Munich/Bavaria is the worst hit, but it does usually drive up airfares from Seattle to anywhere within 200 miles. lol

I'd vote for early September! Prices will be lower, and all the things that closed for the summer will be back open! After the fest is good too, but as you know it can get ccccccccold!

Also, Scanair is halting their Seattle route in November, so less competition might mean higher rates.

As far as I know it starts in mid-end of October, until December, 12th when prices start climbing up.
You can actually compare fares on skyscanner.net

There is usually a date right after labor day where airfares will drop. I usually found it by just putting in a date before labor Day, looked at the price, then put in the one I wanted after labor day and made sure the price had dropped. (It has been as early as September 2 and as late as September 5) It may get even cheaper in October, but unless you are going south of Austria, I would try to go earlier. (BTW- last year the price never dropped. I think this was due to high fuel costs, etc. I think this year will be similar to 2002- which had some of the best prices to Europe do to everyone not wanting to travel after 9/11)

As you read here from responders those dates are not fixed. They vary for every airline, RR line and city.

When you search for air fares, you will see when the rates decline on the line you search. We always travel in Oct or Nov and find rates lower.

Some web pages will define rates on a calendar by month so you can tell when rates go up or down.

Thank you. I am kind-of thinking about spanning the Thanksgiving holiday (but not close enough to bump rates) just to maximize my vacation and minimize the kids' disruption from school.

I always find the best deals in November! That's why four years in a row, I traveled to Europe in November. The down side is that the weather can be very cold, like when I went to Prague and Berlin!
So bring warm cloths if traveling in those places.