In Berlin you probably find the most exciting nightlife of the world. The best areas for nightlife are still Mitte and Prenzlauer Berg. Friedrichshain isn't bad either. All of these districts are in the eastern part of the city. There you find countless small and hip nightclubs, many of them aren't easy to find as a non-local though. So you might ask a local or buy one of the city magazines to see what's going on:

In general it makes no sense to enter a nightclub before 1am. The nightlife in Berlin starts rather late so as a result many clubs are nearly empty until 1pm/0:00. However, at least they are open until next morning. Nightlife in Berlin has an egalitarian tradition, it doesn't matter what you wear, how you look, how old you are. Another positive aspect is that the nightlife is cheap as it can be. You rarely pay more than €10.00 to get into a club. 

A good starting point for a night out in Berlin is the Kastanienallee. There you find numerous bars, restaurants and some great nightclubs nearby. Other good starting points are Kollwitzplatz (Prenzlauer Berg) and Hackescher Markt (Mitte) or Simon Dach Strasse in Friedrichshain.
 

Some great nightclubs:

  • Magnet Club, Greifswalder Strasse 212-213, 10405 Berlin: Stylish club in Prenzlauer Berg. Almost everyday concerts and parties, mainly indie rock/pop, brit pop etc. http://www.magnet-club.de
  • Bastar*d@Prater, Kastanienallee 7-9, 10435 Berlin: A small but hip club at the top of Kastanienallee (near subway station "Eberswalder Str.").
  • Pfefferbank, Schoenhauser Allee 176, 10119 Berlin: A great little club just next to the Pfefferberg (subway station "Senefelder Platz"). http://www.pfefferbank.de
  • KingKongKlub, Brunnenstrasse 173, 10119 Berlin: Great location in Mitte (near Rosenthaler Platz), great lounge atmosphere. http://www.king-kong-klub.de
  • Maria, Stralauer Platz 33-34, 10243 Berlin: One of the hippest places for those who like techno/electronical music. http://www.clubmaria.de
  • Duncker Club, Dunckerstrasse 64, 10439 Berlin: A very small club in the northern part of Prenzlauer Berg. It is not easy to find but really worth a visit especially if you're interested in indie/rock music. http://www.dunckerclub.de
  • ...............to be continued

Helpful links:

http://www.dancefloorguide.de/berlin
http://www.residentadvisor.net