There are quite a few good places in Berlin for concerts. But, more importantly, there are some concert agencies and they book, depending on the band, a club or a hall. So to check out the concert schedule I felt sometimes easier to check these agencies and all the favorite clubs. The agencies are called: Loft Concerts, KOKA36, KarreraKlub, to mention only the favorite ones. Anyway, the following places are my favorites:
Ausland
This is a very cool place. Often some experimental music and other interesting stuff going on (films, exhibitions etc.). I think you could call it Cave12 of Berlin (you will notice more and more that I always reference Cave12 (see Geneva section) because this is just my favorite club). Lychenerstrasse 60.
Knaack
This club is good for indie concerts, but also for indie parties. I have seen here HGH, Kristoffer Aström and others. It's not my favorite club in terms of the building and the decor, but the program is very fine. Greifswalder Strasse 224.
Magnet Club
A pretty small club with a bar dividing the club and a concert section. I am very bad at guessing how many people get into that club but I would say no more than 300. I have seen bands like Granddaddy there. As an indie music listener I would trust this club most, if I didn't knew the band. Greifswalder Strasse 212/213.
Passionskirche
This is a church which hosts indie-concerts in a rather unique atmosphere. If you have the chance to catch a concert there, go and see it. It will enchant you! I have seen Beck there - definitely one of my all time favorite concerts. Zossener Strasse 65.
Postbahnhof
This is the new (although already two years or something old) place for the famous Fritz-Club (there's also a Fritz Radio). I would say, most indie bands that have achieved a certain popularity like, for example, AIR or LCD Soundsystem are playing there. Depending on how big their popularity is they have different stages. Strasse der Pariser Kommune 8.
SO36
This is a legendary punk club in Kreuzberg. I am not an especially big fan of it, but I think it as to be mentioned for its role in the past when Kreuzberg was the place for socialist West Germany. And sometimes there are good concerts there. Oranienstrasse 190.