Berlin just before Christmas and NYE is pretty slow, hostels offer special deals during that time. I know that during Christmas it is relatively easy to get a hostel bed in Berlin, I am less sure about NYE. But if you book in September/October/November and intend to arrive 1-3 days before NYE you should find something.
I also recommend that you arrive a little bit early because a lot of the underground DJ's do not advertise anywhere online, you find out about parties and such from posters in the streets and in the magazines like Zitty and such.
As for hostels I can recommend, check out
Heart of Gold
Meininger (Hallesches Ufer)
Odyssee (www.globetrotterhostel.de)
Ostel (www.ostel.eu)
AO (at Zoo) and Helter Skelter are also supposed to be good. Best location for the party at Brandenburg Gate are Helter Skelter, baxpax and Heart of Gold, as it they are only a 20 min walk from Brandenburg Gate (very close by Berlin standards) and are on a direct S-Bahn line (one stop with S 1, S 2 or S 25 from S Friedrichstrasse to Brandenburg Gate). For other parties the hostels in the East (ostel, odyssee) would be good as they are in relatively hip areas. But basically anything within BVG zone A close to an S or U stop will work very well.
http://www.bvg.de/
As for catching the train from the Netherlands I would recommend breaking the trip up in the Harz mountains, especially if there is snow. If you use regional trains there are special offers you could use, with the Niedersachsen Single ticket it is possible to get from the Dutch-German border near Enschede to the Harz mountains for only 20 EUR.
[ Edit: Edited on 29-Apr-2009, at 12:50 by t_maia ]