I'm looking for something different to see in Munich - something that the average person may not consider top of their must-do list, like the Paris Sewer Museum or the Capuchin Crypt in Rome. Any suggestions? Thanks

Check out Dark History Tours. The guy is not only an archeologist but has all kinds of interesting tours about Munich, stuff you probably wouldn't get on a regular tour. He is also a native English speaker and passionate about the history of Munich,but funny and entertaining too.
http://www.dark-history.eu/

The surfers on the icy creek at the (bottom ?) of the Englischer Garten.

If you are able, do a Mike's Bike tour. Located behind the Hofbrauhaus. It's a different way to see some of the sights and a lot of fun.

There is a small museum, dedicated to the comedian Karl Valentin, with a nice little restaurant inside. Unfortunately no tours in English (just German and French).

http://www.valentin-musaeum.de/offen.htm

Thanks everyone! I'll check 'em out!

I believe every Munich schoolkid has done the tour of the sewers in Großlappen. It's Europe most advanced water treatment plant. You'll have to pre-arrange a tour, they're not open to the public every day. http://www.muenchen.de/mse
It will leave a lasting impression when you see the shit and and the other stuff (You can say shit in that context, can't you? ) and the clean water after the treatment.
And I would also visit the Völkerkundemuseum. It's full of Bavarian history and of course the Oktoberfest-Museum in Munichs oldest building.

And in respect to Karl Valentin, you just have to watch and hopefully understand the "Buchbinder Wanninger" (Bookbinder Wanninger) sketch. This is so true in todays world as well as in those days, when the thelephone was new. In fact I believe this happens to me almost every day... Did you ever speak to someone responsible for anything when you needed help or information from a company? Nothing has changed since then.
"Buchbinder Wanninger" is a figure of speech today.