I like this solution. We have mapping app that exposes annotation tools - although we do not allow users to save, it's something on our radar.
Michael,
I'm not sure of your platform, but if you happen to be using asp.net, and are hosting the map within an .aspx, you can easily call page/web methods from the map to execute server side logic, such as saving the JSON layer to SQL Server by a user id, or session id, and then later re-load it/make available when the user revisits. If this is helpful for you, I can give more information, otherwise, Tim's link mentions some info on dojo.xhr.