Why do some cargo aircraft have windows? There are some cargo aircraft that have windows which are not covered. Look:


On the second deck above where it says "Hong Kong Asia's World City" the aircraft has 3 uncovered windows. Source: Airliners.net
Also here:


Source: Airliners.net

On the upper deck of the Martinair 747 the windows are not covered. My question is: if the aircraft is used for cargo, why do they leave the windows uncovered?
Some cargo aircraft do have limited seating, as mentioned in the comments it could be for the relief crew, load officer, or other employees making a hop on the plane. Here is a nice blog post about  flying in a cargo plane. This article covers it pretty well also. 


(source)

Some cargo planes are also old passenger planes and some of the windows may be left in place.