Favorite place used to be called the Last Drop (there is one in Brighton), it is now the Corner Tavern.
http://www.thecornerboston.com/
The crowd here tends to be a little older (mid 20's and up) rather than a college age crowd - they are probably across the street at Crossroads. It is small, but open until 2. Upscale sandwiches/wraps/pizza available until midnight. Yelp page:
http://www.yelp.com/biz/corner-tavern-boston
Used to go to Crossroads a lot too, but the re-model killled it for me.
Cheers,