Outside of Prague (obviously) I have spent the most time in Amsterdam and Paris. A week is too long for Amsterdam as well, unless you plan to be a full on stoner. Prague has as much or more to do then Amsterdam. I love Amsterdam, but after Van Gogh, Anne Frank and general town exploration, you are out of stuff to do. Especially in late October.
I'm sure there are interesting towns around to visit, so you can do that for a day or so.
If you haven't been to Amsterdam, then I would recommend it, it's a great town, but I would recommend a two town visit for sure. There are very few European cities that merit a full week.
Paris may be the only one. Some might argue Rome, but I begin to hate that place after 2-3 days.
I would do one of the following:
Madrid - Barcelona
Prague - Vienna (although I think Vienna is very overrated, many like it)
Prague - Berlin
One thing to note is that it is really cheap to fly one way in Europe and you could pick any two cities and fly between them cheaply and pretty much anywhere in less then two hours.
So you could go to Amsterdam and Prague or any two destinations. You could do Prague - Dubrovnik and see to great and very different places. There are limitless combinations by flying and it is usually cheaper then taking the train (at least in Western Europe).
Most well known flight sites don't include the cheap airlines. You have to know where to check to find the best deals,
Another handy site is Rome to Rio, it shows all modes of transport with rates:
http://www.rome2rio.com/