Europe in fall - Train Travel etc.

If you have the flexi style of pass, you get a certain number of travel days within a two-month period. Whenever you choose to fill in a travel date, you are covered for travel all day until midnight. If you were taking a very short trip, you could choose to buy that ticket locally, instead of using the pass. Since most of your destinations are served by direct train, that may often be your only train of the day. Passes must be activated in Europe within 6 months of purchase (e.g. purchase on March 20 and activate by Sept. 19). See http://www.ricksteves.com/travel-tips/transportation/trains/using-your-rail-pass for more about all of these topics.

Thalys trains from Brussels to Paris have a high pass holder seat reservation fee and restrict the number of pass holders onboard. For that route, the better solution is either not to use the pass (and not include France on the pass; buy an advance-discount ticket, instead) or else to take the TGV from Lille to Paris, with more cheaper but still limited seat reservation fee. Following the first solution, a pass that you could consider would be a 4-region Eurail Select pass for 5 travel days in Czech Rep, Austria, Germany, and Benelux for roughly $400 per person in 1st class if you have 2 or more travelers (saverpass), or $300 if you're under 26 and traveling in 2nd class. Single adults pay $470 in 1st class.

Thalys and TGV have the only real reservation issues for your route. In other areas, you could just jump on a train with the pass. Full-fare 2nd class tickets would cost about $400 to buy as you go, or you'd get some significant discounts if you locked in advance tickets for specific dates and times (most go on sale about 3 months ahead).

We have done two trips to Germany/Austria in the last two years, using point-to-point rail tickets bought online from the national rail sites (bahn.de and oebb.at) Second class was fine, got reserved seats on days we thought might be busy. Since we knew our travel plans in advance, getting the non-refundable economy tickets wasn't a problem.

"We will probably do a 1 way car rental between Munich & Berlin."

Using the high speed ICE trains will be a far quicker, more efficient and probably more pleasant journey. For example, there's a departure at 08:40, arriving 14:41 (time 6H:01M, no changes). That trip is from Berlin to Munich, so departure times may vary in the other direction.

Hi,

Going between Munich and Berlin, day or night train option, is the perfect time to use the rail Pass since it's on the ICE. That's where a rental car is not needed.

On using up a Pass day: say you take a day trip Munich to Salzburg, then after a few hours there, decide to go on to Linz, the day used is valid for Linz. And returning to Munich from Linz good on that day too, ie once the conductor punches a day on Munich-Salzburg, any rides after that on the same day, you just show that cancelled day to any other conductors when it's ticket checking time.

More favorable is when you do the night train option, say Munich to Berlin on the CNL. After 1900 it's considered a night train, ie reservations are mandatory, even for a seat with the rail Pass. Since Munich-Berlin arrives after 0400, any ride you take on that day of arrival is will not be counted., ie upon arriving in Berlin, you want to take a day trip to Lutherstadt Wittenberg ( a short distance), another ICE ride. For that day trip you don't use another day, same as on the return to Berlin from Wittenberg.

When you go from Berlin to Hamburg ( also short under 2 hrs.) on the ICE, you use a Pass day for that ride, same as presumably going from Hamburg to Amsterdam. Just get a point to point ticket to cover from the German border to Amsterdam if the Pass is only valid in Germany. That's what I did, covering Duisburg to Amsterdam with a point to point ticket.

With your itinerary as listed the Austria-German Pass suffices as along as you have 3 full weeks.

A nice feature of any 2-country pass, like Austria-Germany, is that it allows anyone to choose a cheaper, 2nd-class version, while the 4-country Select pass only comes in 1st class for travelers age 26 and older. If you don't have many stops planned between Munich and Berlin, then certainly train is the easy choice and a good use of a rail pass day.

You're wanting to visit 8 cities in 3 weeks, and I'm afraid your trip might be a little bit of a blur.
You'd do best to take Austrian Airlines from Toronto to Vienna, as Prague Airport is not much of an international airport. It's also a better starting point.
You can easily take a train from Vienna to Prague to Berlin to Hamburg. Amsterdam to Brugge to Paris is another straight run. Unfortunately, Munich is off the beaten path with the other cities on your itinerary.
Every city on your list is a great European city, and well worthy of 4 days in each place. You really need to limit yourself to less cities and simplify your trip.