There is a website called www.wg-gesucht.de where you can find rooms in shared apartments (WG = Wohngemeinschaft; you may change the language at the bottom of the page).
There is student housing by Studierendenwerk (www.stw.berlin) that is affordable but demand is much higher than supply.
Berlin boligutvikling - good condition and quite close to the university, although a bit expensive.