Berlin is a big city with several local gay areas. The main area with most of the gay bars is Schöneberg, Most gay bars are located near metro station Nollendorfplatz (see map). There are many gay shops here and nice gay restaurants and lunch rooms.This is also a very central area, with the main shopping street nearby. The metro runs 24 hours, so you can travel from here to other parts of the city. Taxis are not expensive either.
In this area you find many gay hotels.