I am having a hard time finding an affordable place available in Munich at the end of September because of Octoberfest. ANy suggestions?
Stay outside of Munich proper and use their train system.
Hotels in Munich have been booked for months because of Oktoberfest. We got ours last November. There may be cancellations once things get going but you'd be better off staying outside of Munich.
Munich hotels double their prices during Oktoberfest, because they can. It is not a good time to visit unless you are interested in the festival. Then you have to pay the prices, or stay outside the city and commute in.
Are you trying to stay in Munich to attend Oktoberfest events, or are you just passing through? How long will you stay and from where, and to where are you going? A few years ago, I stayed in Landsberg am Lech on the last Saturday night of Oktoberfest. There were rooms available, and they had not raise their rates, but they were an hour by train from downtown Munich.
Consider booking an apartment through a service like Wimdu.com. I used this in Vienna. I shopped apartment rentals in Munich for the same time period you are seeking through Wimdu but did not find anything to my liking. I did eventually book an RS recommended hotel in Munich at premium prices. Also try homeaway.com or airbnb.com. https://www.airbnb.com/s/Munich--Germany?checkin=09%2F29%2F2012&checkout=10%2F01%2F2012&guests=2