Berlin,
Of course the brandenberg gate with milling humanity, usually good street shooting nearby and maybe an organ grinder. Nearby the holocaust memorial is quite touching, just an array of stone rectangular prisms of varying heights but even tops. See people interact with a stone maze.
Walk the length of Unter den Linden and rest your feet at any of the numerous cafes. Ogle at salvaged pieces of the old "Wall" which are used as decoration in front of the occasional shop
In the twilight, catch the Kaiser-Wilhelm-Gedächtnis-Kirche to see some light-play on a WWII ruined church that is still in use, although in a refurbished state.
I enjoyed the Berlin Zoo, a very nice collection, but you are there at an unfortunate time of year.
Be sure to go to the Gernam Kristkindlmarkts, of which you will find (I think) three in Berlin. Although I prefer the intimacy of Munich's MarionPlatz and the stands surrounding the Rathaus, Berlin is somewhat more cosmopolitan.
I fear that you may be less impressed with photo opportunities this time of the year, but the street shooting is always good.
As for Prague, since I was there just last year, their market is more a New Years market than a christmas market since during the long Soviet era, most of the christmas festivities were secularized and moved to the new year.
Mold of the old town square is great to shoo, particularly at night. Be sure to go to the Jewish Quarter and shoot the new Synagogue, which is actually quite old indeed.
The street that runs from the Old Town square through the Jewish Quarter is Boutique row, so it resembles similar streets world-wide.
Take in the Fred and Ginger building and walk across the river. Take the funicular up the hill for an overview of the Old city from the other side.
GET OUT before New Years if you are at all claustrophobic, as I said, it is High Season there.
Please take note of the Art Deco decorated architecture (Mucha-style) which is practically everywhere
Take a bus ride and get out of town to take in a few nearby towns and maybe even the Ossuary, a macabre sight indeed.
I filed a few of my shots here
http://www.flickr.com/photos/rwfreund/sets/72157603599910201/
Have fun, and remember to get out and walk around early when everyone is still sleeping, it is a very different place.
-bob