Closed: Box Tree, Alley's End, John's Pizzeria (Lincoln Center)
The new Zagat Wire (Yes, I subscribe. Shoot me.) has a list of closed restaurants that caught my eye. Box Tree was, I believe, a restaurant that had bigger union problems than even Tavern on the Green or Cipriani and was picketed by the unions for multiple years, if I recall. I'm surprised that its closing wasn't picked up by the Times, NY Mag, etc.
Alley's End was always a favorite of mine for the quiet scene in Chelsea. John's Pizzeria, well, I always thought that was an odd location for such a big pizza space...
Closed: Alley's End, Alva, Atlas, Box Tree, Cello, Eli's, John's Pizzeria (West 65th Street location), Pintaile's Pizza (Fourth Avenue location)