A target sector is a sector in a map that is the focus of a manipulation of some sort, caused by a control sector and its control linedef. An FOF, a conveyor belt, and a crusher are all examples of sectors that have been affected, and in editing terms, are called target sectors.
Target sectors don't necessarily need to be inside the map. Some linedef executors need to change aspects in a control sector, and thus the control sector is tagged so it can be changed by said linedef executor. This control sector is also a target sector.
When editing a map, you know that a sector is a target sector because it has a tag number other than 0. This tag is what connects the target sector with its control sector. Target sectors can have more than one control sector at a time, and a control sector can have more than one target sector at a time.
Some map editors give a target sector a particular color (generally green or yellow in default settings, although this can be changed) to indicate that this sector is special. But, in order to view it in said color, one must first hover the mouse cursor over the control linedef. Otherwise, a lot of the map would be green, and that could be a bit distracting.
Some target sectors can only perform their action when they have a particular effect. A notable example are conveyor belts, where the target sector must have the Conveyor Belt sector type to work correctly. Other examples are speed pads and rope hangs.