I personally love Mother Fool's CoffeeHouse. It's quite a walk from campus, the crowd is fun and the tea/coffees are amazing. There is almost always a musician on stage. I even heard the place is now hosting magic acts!

http://www.motherfools.com/index.php?uri=home
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Give Michaelangelo's a try. Besides having an artistic/ninja turtle sounding name, it has great coffee and is just an all-around awesome place with a good location:

http://maps.google.com/maps?hl=en&client=firefox-a&rls=org.mozilla:en-US:official&hs=OXg&um=1&ie=UTF-8&q=Coffee+SHops+Madison+Wisconsin&fb=1&split=1&gl=us&view=text&latlng=2989679877628711552
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I recommend Zuzu Cafe. It's warm and colorful and full of options. In addition to coffee, there's a great selection of beer and wine, and a fantastic menu with sandwiches, tapas, dinner specials, and ice cream. There's often music on the weekends if you're so inclined. Zuzu is in the Vilas Park neighborhood, reasonably far from campus -- and close to the Arboretum if you fancy a beautiful walk before or afterwards.
Source(s):
http://www.thezuzucafe.com/

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