Itinerary help

If you are in Berlin for 5 days, consider doing either a walking tour or a bike tour rather than a hoho tour. You will have a better orientation and have a great introduction to the history of Berlin. It is the best way to cover many of the sites most tourists want to see. You could also add in a visit to Track 17 , Wannsee Villa, or the Olympic Stadium. While there, take a trip to Sachsenhausen Concentration Camp or to Ravensbruck Concentration Camp. I personally found the presentations in both of these KZ to be of a higher quality and more interesting than those in Dachau. Ravensbruck especially really got to me as this was a camp basically just for women.

A day trip to Potsdam would also be well worth your time. The palaces at San Souci are gorgeous and the park around them is interesting in its' own rights.

The tour company I have used my past 5 visits to Berlin is Insider Tours.
http://www.insidertour.com/

I agree with Ms Jo that a walking tour is better than a HoHo for Berlin (I've done both; what you miss on the bus is the history, and the intense concentration of important events in a small space over the years of the 20th Century). If you look at the walking tour company's websites, you'll see that they have general tours, Nazi era tours, Communist era tours, gay history tours, Jewish Berlin tours, etc. A general one is the best way to start, but you may also want to do a second one to get more deeply into a special interest.

Since you're interested in history, budget as much time as you can for the German History Museum in Berlin (a full day isn't too much; a half day is minimum).

Instead of Checkpoint Charlie (disappointing museum and not much to see on the street), be sure to see the last remaining section of the double wall construction of the Berlin Wall. That's the Bernauer Strasse section near the Nordbahnhof station. The station itself has a fascinating exhibit on "ghost stations" and escapes, and the free films at the visitors center were fascinating too. By the way, this is all much more impressive than the East Side Gallery (the other remaining sizable section). If, like me, you're fascinated by Berlin's juxtaposition of many pieces of its 20th Century history in close proximity, there's a small section of the Wall right near the Topography of Terror.

There's also the DDR Museum, which is better than the Checkpoint Charlie Museum.

I wasn't as taken with the zoo as most seem to be, but the aquarium was great.

I didn't care for the Botanic Gardens, and the Gamäldegalerie was somewhat disappointing. If you're looking for something different, the Soviet War Memorial in Treptower Park is certainly something to see.

Eat some Bratwurst while in Nürnberg. Schweineschäufele is great too and a Franken specialty. Unfortunately no Biergartens will be open in October. Walk around the old city along the Pegnitz river and check out the Albrecht-Dürer-Platz too. There is also a nice German Toy museum in the old city center.

http://www.bratwurst-roeslein.de/de/
http://die-nuernberger-bratwurst.de/
https://museen.nuernberg.de/spielzeugmuseum/
http://www.museums.nuremberg.de/
http://www.schaeufele.de/index.html

we just got back from our 2 week Germany trip and we spent about 4 days in Berlin. It's a great city. We did the HOHO bus just to be able to get acclimated to the city and use the transportation around the city. We bought the entire package so we could make it out to olympic stadium (I recommend going up to the bell tower for the views!), but I do feel like we wasted a lot time on the bus and if you don't have an english speaking guide it's really kind of lame (some of them have pre-recorded audio or the live guide--who speaks in both languages--will speak a lot for the Germans but only give brief descriptions for the English speakers). The reichstag was really cool and we went up in the dome, but i registered at least a month in advance so make sure you do that ahead of time. Checkpoint charlie is really only worth stopping by for a picture, its so touristy there. The topography of terror is worth a few hours or more if you are interested in that part of history. We stayed in Prenzlauerberg which is very close to some of the remaining sections of the wall and is an awesome little neighborhood with lots of nice cafes, etc. We went to the Prater beer garden twice and enjoyed the ambiance, food, and beer both times. We didn't come across any Americans while there, so it seems to be a nice local gathering place. Royal 44 also makes an incredible doner sandwich and the owner is super friendly and speaks good english. I had about 5 different doners while in Germany and that was probably the best! Munich is also a great city, we did all the historical sites and really enjoyed the English garden. I highly recommend the day trips to Salzburg and to the Eagle's Nest in Berchtesgaden.

Berlin is a great city to bike - Fat Tire ha a great tour and you can keep your bike for the rest of the day. It is a a good way to get an intro to the city - my DH did it no problem at 75.

Either way be sure to go to the Holocaust Memorial - very moving.

The Pergamon Museum is a don't miss

Another vote for the Berlin walking tour. We did hop and off the train/subway while on the tour. But so much we would have missed had we not taken the tour.