Will be in Berlin for six days in September. Looking for lodging suggestions...and other ideas about the area you care to share.
I would look in to an apartment as you will be there for a good amount of time. Most apartments rented to visitors are in Prenzlauer Berg, Kreuzberg-Friedrichshain, or Charlottenburg. All are incredibly close to Berlin's magnificent transit system, but a bit farther from the sights. There are plenty of places to eat and drink in each of those neighborhoods, and all of them are extremely safe. Charlottenburg is in the former West Berlin, which has become more sedate in the past decade. Prenzlauer Berg and most of Kreuzberg-Friedrichshain is in the former East, which is much more lively and trendy. VRBO.com is a great place to apartment shop, with good pictures and information.
We stayed at VRBO..List?ing #196584 which is in the Tiergarten area of Berlin. I don't know what size apartment you require, but I can absolutely recommend this one. The owners, Christa & Elias, are fabulous. I have rented many apartments throughout Europe and the US. This one was the best. This was our second trip to Berlin and we spent a lot of time exploring all the different areas. We loved this one. Very convenient, but also a real Berlin neighborhood.
I rented from Berlin Habitat (berlinhabitat.com) in May/June. I was very happy with the accommodations. The owner was quite easy to deal with (paid with credit card, sent detailed directions, apartment very clean and well equipped). I loved the location. They have a number of apartments and there are quite a few reviews on tripadvisor (including my detailed review).
If you are considering a hotel, I was on a Rick Steves tour in Berlin last fall. We stayed at Hotel Kastanienhof www.kastanienhof.biz in the Prenzlauer Berg area. The hotel was typical Rick Steves: clean, friendly English speaking staff, good breakfast, (ask for a room away from the street) located close to transportation, good restaurants in a safe neighborhood and only about 3 blocks from the Prater Garten biergarten www.pratergarten.de almost everyone speaks English in Berlin.
Kevin, I was in Berlin last year and would highly recommend Pension Peters. It's located in the area between Bahnhoff Zoo and Savignyplatz, so transportation is very accessible. The staff are exceptional and there are lots of interesting restaurants in the area (including Schwarze's Cafe which is open 24-hours and only a few doors down from the Pension). If you're planning on taking any tours, The Original Berlin Walks meet in front of the McDonalds across from Bahnhoff Zoo, which is an easy 10-minute walk from the Hotel. I took several tours with them, and thought they were excellent. The Guides have an exceptional knowledge of the history. Happy travels!
It really depends on your style and what sights you're most interested in seeing. Rick Steves and a lot of people on this board tend to favor staying in the west, near the Zoo/Tiergarten/Charlottenburg area. While it is nice over there, I find that most areas of interest aside from the zoo/garten/ku'daam are a somewhat annoyingly long/confusing transit ride from the west (maybe because of the construction on U-bahn lines when I've been present) and as such I would recommend staying in the east. It also really depends on your budget. Berlin is cheap by European standards, if you're willing to stay a bit from the mitte in a "colorful" (but interesting!) neighborhood like Kreuzberg-Ost or Freidrichshain you can save a lot of money, but again, longer rides on public transit. Prenzlauerberg is a nice centrally located neighborhood. The Mitte area is as well (obviously) but can feel a little dead at night depending on where you are. As far as ideas, sky's the limit. Berlin has a ton of things to do and see depending on your interests.