I don't know much about Portland, other than they are starting to install bike boxes.
In NYC there is no turn on red. Many streets are one way. Many bike lanes are on the left-hand side of the road (I think this is to lower the chances of getting doored, and on to avoid the bus lanes on the avenues). Given that environment, often times a NYC cyclist will approach a red light in a bike lane on the lefthand side of the road. If he intends to make a left, there is no problem, but if he wants to make a right, it can be a little trickier. The bike box creates a buffer zone during a red light to change sides or move foreward without interfering with pedestrian space.
In NYC they are not installed everywhere, but rather where they are deemed to be most useful.