Berlin is a family-friendly (and very accessible) city.  Commuting is not a problem when you have small children and strollers - most stations serving the tourist attractions have elevators (if they don't, you can be more risky and use the escalators).  The trains and buses have designated places for strollers, wheelchairs and bikes.  The 100 and 200 buses take you to the attractions without having to pay the steep price for a sightseeing tour bus which is around 15-20 Euros. During rush hours though you may have to wait a little while for the crowd to thin out.

Long lines can also be avoided at the Reichstag and the Memorial for the Murdered Jews of Europe.  The Reichstag has a separate entrance for families with small children and people with disabilities at the right side of main entrance/steps.  A separate elevator entrance also provides access to families at the Memorial.Just tell the guide that you have small children and they will direct you to the separate entrance.