Progress Coffee, a nice space just east of the highway.
Rio Rita, on east sixth street, is a coffeeshop/lounge so it's a good choice if you're a mixed group with some people who want to work and others who want to lounge.
Jo's Coffee also has a location on South Congress, but that's outside, so it's better for people watching than for anything approximating work.
Halcyon--I'm not sure why I put this on the list, because I never go there, but it is a coffeeshop near downtown Austin.
BookPeople's coffeeshop is a good quiet space with access to books and magazines. It's also across the street from the Whole Foods flagship, which is epic and a great place to eat.