Amuse-Bouche put together this informative mashup of BYOB establishments around town. These are places that either allow you to bring your own for free, or have low "corkage" fees-- that's what they charge you to open the bottle in the restaurant. Much of the data is drawn from the NYMag BYOB list, so it may be a little bit out of date.
Much of the recent interest in BYOB stems from the problems the East Village restaurant E.U. has been having with the police-- they've been denied a liquor license, and they've now gotten in trouble for letting people bring their own bottles. Why? Apparently BYOB requires a license if the place is larger than a certain size. The Villager reports:
But Bill Crowley, an S.L.A. spokesperson, said that, according to Section 64B of the State Alcohol Beverage Control Law, only places with 20 seats or less can legally operate B.Y.O.B. without a license. He said there is a license that must be obtained to allow restaurants with more than 20 seats to operate B.Y.O.B., but that it’s just as costly and time consuming to get as a beer and wine license, so most applicants apply for a beer and wine license instead. E.U. has more than 90 seats, according to Stetzer.