We have a welcome-home ritual when we return from the East Coast, landing @ OAK or SFO around 10-11 pm, to grab a drink and a late meal en route home (which is in south Berkeley).
We usually go to Fonda, which is open until 12:30 am. The duck tacos and margaritas are generally worth the detour, but nothing else on the menu really sings these days. Once we tried Rudy's Can't Fail in Emeryville, but the 'hood is a little sketchy @ that hour.
We'd love some other options for places that have great food and are open past midnight in the East Bay, especially in south Berkeley or north Oakland.