The Prince Charles Cinema in London, UK [1] is also doing this kind of thing and is about the only place I can be bothered to go see a film these days.
There's quite a few independent cinemas in UK cities, all doing that sort of thing - many of them are non-profits as well. Fewer screens than multiplexes yet a more eclectic choice.
And like the Alamo Drafthouse, the Parkway and the Cerrito Speakeasy in the East Bay were doing something similar...though they closed in the economic downturn.
[1] http://www.princecharlescinema.com/