If you are at blackhat europe (in Amsterdam) there are basically three ways to go to Berlin.
The main-station in Amsterdam is only a 10 minute walk away from the location where blackhat will be. Just go out of the Hotel, cross the dam square (the place right in front of the hotel), when you are about to cross the tram track go right, keep going, you will walk directly towards the trainstation. You can also use the tram for just a few stations (2 or 3 stations i think).
The best way to find a train to Berlin is online via www.bahn.de. Prices will range from approx. 80-100 Euros (regular rate). Travel-time will be 6 to 8 hours depending on your connection. There are quite a lot of possible reductions in price (if you book long before, if you are under 26 years old, if you have a rail-plus pass,....), watch out for them you can save up to 70% of the normal fare rate. You can order your ticket online, pay by creditcard and get your tickets by post (mail). You can also just buy a ticket at Amsterdam Trainstation. There is also the possibility to download an online ticket, and bring the printout to the train. Getting your ticket online requieres a registration. There is some more information at the international guest page of the german railways.
Berlin has several stations, the best station to go to is "Ostbahnhof", which is only approx. 1500 meters (1 mile) away from c-base. From Ostbahnhof you can take a 3 minutes cab ride to c-base, or you take the S-Bahn to "Jannowitzbrücke" (1 Station) and walk to c-base (approx. 5-7 min.). It is also possible to walk to c-base in about 15-20 min. S-Bahn will be 1.20 Euro, cab will be around 6 Euros, walking will be free ;-).
I suggest, go to mapquest.com and get a route. Note: places to park are not everywhere available, so finding one can be difficult (depending where and when), this is true for Amsterdam as well as for Berlin.
Well, I guess you know how to do that, go to your airline, get a ticket. Traveltime will be 1-1.5 hours, if you take the time to and from airport in, it will be 3 hours or more. (hey train is also only 6 hours, less than 7 if you calculate the time to and from the station in.) For information about how to find your way from the airport to ph-neutral see the airport page