This is a great thread and some great responses. This is a tough question to answer because it very much depends on the river and boat types. Here are some generalizations that I've learned from commercial guiding:
1. It's good to put your best boater first. They'll set a good line, set the pace for the group, and are least likely to have a swimmer. If the lead boat has a swimmer, there is no one downstream to help with recovery. (safety kayakers are a good idea when there is a chance of the lead boater having a swimmer in continuous water)
2. I like putting the second best boater as the last boat. This person usually carries first aid and rescue and will catch up to the scene of any rescue. This person can take charge when the lead boat is around the corner.
3. In general you want boats to be close enough to help each other with a swimmer (or flip) but far apart enough that boats don't pile up. That distance is judgement call learned from experience and depends on the type of water (big water, low water, pool drop, continuous, easy, hard, etc)
4. Boat types and personal style is a factor. Oar boats that pull through rapids move much slower than kayaks. Some people like to pull and others like to push. This can cause pile up and distance problems that propagate through the whole group. If you're going to run hard whitewater you want people who can run rapid with a variety of styles and work as a team.
When teaching this to younger guides I describe the boats moving downstream as a slinky. Boat spacing is always fluid and changing and a change at the beginning affects the end. Boat spacing is something that everyone has to have in the back of their mind in order to do it right.
In my mind the ability for a boater to work together with a team and maintain proper boat spacing is what makes them a Class IV boater. I paddle with a lot of people who can make it down Class IV rapids, but I consider them Class III boaters because they're unable to maintain proper spacing in a group.
Northwest Rafting Company