Rail pass or individual tickets?

Do not use the estimator map, it is not current. Accurate pricing can be seen using indivdual rail sites, Belgium, Holland and Germany. If you commit to a specific train, especially going from AMS to BER, you'll see big savings over RS estimator map. Unlikely a rail pass will pay off. Trains will not be full, but you'll save by buying the long leg now.

For just three rides (one of them on a cheap local train), individual tickets are the way to go. For Brussels to Bruges, there are local trains, 2 per hour, with no discount for advance purchase. So, just buy the ticket when you need it. BTW, the ride only takes an hour, so you're right that this is not "extended travel" For Bruges to Amsterdam, there are two possible routes: via Antwerp or via Brussels. For the leg to Amsterdam, you'll be on the Thalys, and this train uses "airline pricing." It's cheaper if you buy a non-refundable, non-changeable ticket in advance, and potentially very expensive if you buy on the day of travel. To find routes and buy tickets, use http://www.b-europe.com/Travel. For Amsterdam to Berlin: You can find prices and tickets on the Netherlands International Rail site: http://www.nshispeed.nl/en. Again, there are discounts for advance purchase of non-refundable tickets.

The Deutsche Bahn website is showing the best price of 39 euro for direct Amsterdam-Berlin trains. Buy at www.bahn.de
Brugge-Amsterdam using the Thalys from Brussels looking kinda pricey. Use local/regional trains through Antwerp and Rotterdam.