A place that serves after 11 pm...
The Franklin actually serves till 1:45am. Wines by the bottle are a bargain here.
Anchovies (South End neighborhood bar serving pedestrian but value-priced Italian-American), 2am. Not a wine lover's place.
Lucca Back Bay (upscale Italian), 1:30am. Extensive wine list.
Via Matta (another upscale Back Bay Italian), enoteca menu till 1am. Another good wine list.
Bistro du Midi (Back Bay, Southern French) has a first-floor bar that serves a limited menu until midnight on Thursdays. Very good wine list.