I'm in Berlin right now, will type a list here of what I would consider must-see here... (hope you adore minimal techno though)
(as Cogent mentioned) --- -Berghain / Panorama Bar --- also check out SUB:STANCE on 11th July there.. but make sure you go there on a techno night especially... that's THE ONE!!
-Bar25 -- also plays minimal... probably best place to go for afterhours chill... like after u been raving at berghain from 6am til 3pm, then hit bar25 or so...
-Watergate --- more touristy but they kill it downstairs usually, upstairs is more your tourist thing... still definately must-check thingie...
-Goldengate --- minimal as well

worth checking out, nice smaller place..
-Hard Wax --- for records obviously...
and area wise I would definately go around Kreuzberg and Neukoln... and Friedricshein as well even tho its got a bit trendy and touristy now I hear... still, amazing graffiti n nice lil shops... check out the lil stage Mullerbuhne or whatever its called near the bridge, they might have some live jazz on...
too ill, can't remember more now, will post if i remember somethign brilliant
u guys will love Berlin tho -- fantastic city!! personally i'm sooo looking forward to Prague later this summer hopefully
