Just messing around with the API some more, here is a little utility to save and retrieve selection sets. It stores them in a text file located in the same location as the project file. The text file has to be the same name as the project file with " SelSets" added to the end. It will create that way automatically, but if you move or rename the file you will have to do the same with the txt file to retain your selection sets.
In the case of a worksets project it will store the txt file at the central file location.
The only small bug is that if you rename a selection set, you have to exit out of the dialog box and restart before you can select that set. I'm not sure why that is yet, but it's a minor thing in my mind, so I left it for now. If I get time later I'll come back and see if I can fix it.
Let me know what you think!