You can also look for the triangles on the system map, which indicate a visible alien force present. Only bother checking for colonies in systems which have an enemy presence.
Originally posted by Kamog: How about going to the colonies screen (F5)? All the colonized moons and planets are listed there and you can click on those.
Is there any other viable way of handling one's colonies?
No, other than the construction window and right clicking on individual colonies to see their stats... Both windows do have numerous view options though...