For a college town, Ann Arbor is sadly lacking in the late night eats department. But the Aut Bar in Kerrytown's kitchen is open until 1 am most nights! Good to know. We went there Sunday night when we were looking for cheap eats downtown and got to Sabor Latino at 9 pm just as they were closing. Aut makes excellent burgers (both of the beef and tempeh variety - my vegetarian friend says they do the best things with tempeh anywhere). Fries are great - made with real potatoes. My other favorite is the BLT-squared - a wrap with bacon, lettuce, tomato, mayo and hard boiled egg.
Aut is also a great place to get Sunday brunch - they do a mexican brunch, with huevos rancheros and huevos con pappas, and omelettes with quacamole. Very good, but usually very busy.
Best to go in good weather - there's not much room indoors, but the outdoor patio just gets larger and larger, and they've just bought all new patio furniture that's really quite comfy and sturdy.
And yes, as you'd expect from the name, Aut Bar is an establishment aimed at the local queer community. But as long as you aren't a raging homophobe, don't worry about it - I go there with queer and non-queer friends alike, and we always have a good meal and a good time.
 Note that this is used as an inclusive for lesbian, gay, bisexual, trans etc, rather than in any derogatory fashion.