While some varieties have inherited a tendency to green shoulders, if you are seeing yellow shoulders it is likely that the upper portion of the fruit has inhibited lycopene production. Lycopene is a plant pigment which gives tomatoes(and watermelons) their red color. The most common reason for the inhibition is heat or sunlight. Ideal temp for lycopene development is 65-75 degrees, but who's got that in August, eh?

What happens most often for me is when blight starts setting in towards the end of the crop and leaf cover decreases. This allows more sun to strike the top of the fruit and both raises the fruit temperature as well as stopping the lycopene production. Carotene, the pigment responsible for yellow and orange in fruits is also present in tomatoes, but is less affected by the heat and so the fruit portion without lycopene appears yellow.

I sometimes get fruit with yellow stripes, especially those in full sun. I've noticed that the variety 'Arkansas Traveler', a "ripe-when-pink" tomato seems more tolerant to sun than most varieties, and side by side with 'Celebrity', it is bearing beautiful fruit with proper coloring.

So, it seems that the way around green shoulders is to select a variety less prone to it, maintain good leaf cover if possible(maybe dense planting and less pruning), or air conditioning the field and setting up small parasols for each plant on sunny afternoons(yeah right)!

Hope this helps, and BTW, I enjoyed looking up the answers because I'd wondered about the same thing myself, probably all of us have some funny looking tomatoes later on in the season.