Usually I check Google Maps, but it doesn't have routing or train times for Berlin. Is there an official trip planner? Bonus points for suggesting mobile applications as well.
You want bvg.de. It has English and German versions, and if you visit the site on a mobile device it'll offer a mobile optimised version. They have an excellent trip planner, covering regional trains, S-Bahn, U-Bahn, Bus, Tram and walking. You can also download various network maps for offline use.
In addition to the website, there are a number of apps available for mobile which work with their data. I quite like the DB Navigator for the iPad, which covers all of the Berlin BVG transport too, but I've seen lots of others in use too!