Some plugins let you have more than one world so......... Someone could make a plugin that would let you have plugins in different world e.g Factions plugin on one world and sky block on the other!
Caxtor http://dev.bukkit.org/bukkit-plugins/perworldplugins/ Took me 2 seconds to search it on Google.
Caxtor PerWorldPlugins like bwfcwalshy suggested. Or per world permissions to disable functionality in certain worlds.