As far as websites go,
www.wg-gesucht.de is the most comprehensive, though Craigslist is also worth a look (http://berlin.en.craigslist.org/roo/). In my experience answering other people's ads is more effective than placing your own. And if you get an appointment to view, bear in mind that the whole process is quite interview-like here, so be charming and enthusiastic! (It took me quite a while to twig that my British technique of showing complete disinterest wasn't getting me all that far...) Also, this might not be so much of an issue for a short-term let, but it can take longer than you think to find somewhere to stay, so try to set up appointments before you arrive so that you can launch straight into viewings when you get here.
You'll see ads posted on noticeboards around university buildings, too - you don't say where you're doing your course, but there's bound to be something like that.
Good luck!