The Van Gogh museum is closed when you are planning to visit. The main paintings can however been seen at the Hermitage Amsterdam.
Go to the museum website for more details. Also see my earlier post:
http://www.fodors.com/community/europe/amsterdam-museums-re-openings-and-a-temporary-closing.cfm

Um, is there some special reason for Bavarian food. Berlin is NOT Bavaria - and the local food is just fine.

I would look for cheap flights from Berlin to Amsterdam.

We arrive in Berlin on 28 December for 4 nights. It is our 6th visit and we love the city and all it has to offer.

As mentioned above, Berlin is not in Bavarian. The city does have lots of great restaurants. What neighborhood are you staying in?

Look into the Berlin Welcome Card with Museum Island.

For us, a couple of days in Amsterdam was adequate. I suggest booking tickets in advance to avoid long lines. We were very happy we did.

For must see activities in Berlin, read the many trip reports on this forum.

< I suggest booking tickets in advance to avoid long lines. >

This was in reference to Anne Frank House.

if you can, I would spend more time in Berlin and fly to Amsterdam

Um, maybe because they want Bavarian food. Whether the local food is "fine" or not, is not the issue.

I am sure the OP appreciates both your geography LESSON and your condescension laced defence of the local food.

For Bavarian food in Berlin try Weihenstephaner, at Hackescher Markt, or Maximillians, on Friedrichstrasse, near Gendarmenmarkt. There are many more you can find by searching for "Bavarian restaurant Berlin" in Google, but these are the only two I have been to.

You have 4 nights in Berlin and 5 in Amsterdam. I would have reversed that, but that would have you moving on New Years eve which you probably don't want to do. Having the extra day in Amsterdam is not bad, because there are many places you can day trip to like; Delft, Leiden, Den Haag, Utrecht, Haarlem and Alkmaar.

May I make a suggestion?

Christmas markets are actually something to just note and move on. You've got plenty of Christmas hooplah where you come from. There are unbelievable, one of a kind things to see in Berlin. The Reichstag Dome is a place you should plan to see. Right now, Germany is the most powerful country in Europe, and much of the fate of Europe (again!) is being decided in the Reichstag, and its a pretty fantastic building that represents the unity of Germany after the Cold War. So dont miss that.

I also suggest that you don't miss the Museum of the Berlin Wall. If you are Americans, and maybe even if you are not, that wall defined the western world for decades. It's actually a really well-done museum, with videos and explanations, but most of all, the wall is right there.

Finally, the Red Light District is what it is, and people think it is funny and all, but the women there have had lives that are awful, really. To me, it is like going to the worst kind of zoo -- and zoo animals are better cared for. Maybe you come from someplace where prostitution is hidden, so you want to see what it looks like when it isn't. If you think for a second, you can imagine. I find it grim.

The 6-7 hr train ride to Amsterdam is rather long & boring, but it could be very very cheap if you pre-purchase the international city ticket deal (I remember seeing it advertised as low as 29-39 euros instead of the regular €110-135, check www.bahn.de for this year's deals), but it would cost a lot if you want the couchettes to sleep on, so I would not recommend an overnight train because you won't sleep well plus there is a train change after 3 or 4 hours either at Hannover, Duisburg or Hilversum. I would recommend taking the late afternoon train as darkness sets in early anyway (eg: 2:49 -9pm or 3:50-11pm trains). If you value your time I would then second kfusto's recommendation to fly a cheap airline although flying into Schiphol is never that cheap (compare to other cities) unless you fly to the cheap airport near Rotterdam( can't think of the name).

There are 25 Christmas markets in Berlin, most tourist go to the two sparate markets in Alexanderplatz area in the Mitte, near the Kaiser Wilhelm's church ruin in Charlottenburg (West Berlin), they import snow for the snow slide for the market at the Potsdamerplatz (Salzburg style with Austrian hut where you can eat Salzburger/Bavarian food). I have also seen the market near the Oranienburger street another one between Nordbahnhof & Gesundbrunnen U bahn stations. After Berlin I never can appreciate Christmas markets anymore due to overload, they are practically unavoidable, but I still enjoy them for drinking beer and snacking in a festive atmosphere ( no matter how artificial). It cuts the dreariness of winter in Berlin. I've seen a couple small Christmas markets in Amsterdam which become so negligible if you arrive after Berlin. The street Christmas lighting can best be enjoy if you sit upfront on top of the double decker public buses along Unter den Linden.

The Intercontinental in Amsterdam is just about the nicest grand hotel where international celebrities stay right against the Amstel river whereas the one in Berlin is just OK. It does have a great Michelin star restaurant on the top floor, beyond that I'm not too happy with the ugly architecture and location compare to other hotels. I would almost save the Intercontinental miles and pay for better 5 star hotels which are relatively cheap in Berlin compare to other metropolitans unless you just have an overabundance of Bass hotel points.
I also enjoy Bavarian cooking but Berlin offers a lot of high cuisine at much lower price points, they are bargains compared to those of comparable quality in Paris or London.

We are doing a very similiar trip and would like to jump in here with some additional questions.
Leaving Dec. 16th - arriving in Berlin Dec. 17. We are staying at the Melia for 4 nights. Leaving for Amsterdam on the 21st. I really need help here because you cannot book online train travel after Dec. 8th...WHY?? I did find another train and tickets were $200 plus pp. Any help would be appreciated. DB-BAHN has tickets up to 12/8 for as low as $59.00 from Berlin to Amsterdam. (won't let you book after 12/8)
Staying at De Roode Leeuw Hotel Amsterdam for 3 nights.(12/21/-12/24)
Taking Thalys Train to Paris on Dec. 24th.
We will stay 3 nights in Paris, Christmas in Paris! And, fly home on December 27th.

My 21 year old daughter and I are making this trip together. We have never been and she was very interested in Berlin and the Auschwitz history. Also, wanted to visit Amsterdam! So this is our dream vacation for Christmas. It was much cheaper to do the bookings myself after looking at "packages".
Everything is settled besides the transportation to Amsterdam from Berlin. I would rather not fly but have looked at EasyJet in case we have to. Would rather go by train!!!

Any suggestions on what I have said are greatly appreciated.
Cheers to you all!!

As you know Auschwitz is a long way from Berlin.
There is quite a bit of Jewish history in the city, including museums and monuments.

Sorry! I meant sachsenhausen memorial tour! But, can you help me with the travel to Amsterdam? And, can you help with other things to do in Berlin?

Sorry, never traveled by train to Ams.
Melia is a great location...stayed there twice
You are next to S and U bahn stations. The
public transit in Berlin is excellent.
I would book a restaurant at the top of the
Reichstag Cupola or a tour of the building
Depends on your interest:
there are museums
and important monuments in walking distance of Melia.

<And, can you help with other things to do in Berlin?>

Pull up the many trip reports on this forum for ideas on things to do. It depends on your personal interests. Here is mine from a visit a few years ago:

http://www.fodors.com/community/europe/trip-report-4-fabulous-days-in-berlin.cfm

We are headed to Berlin in December for our 6th visit and will be staying at the Melia for the third time. Great hotel, very good staff, perfect location.