I transitioned the social analysis application to http://socialgraphanalysis.appspot.com/ last week. It turned out to be quite easy. What I came across was this (among others):
When the application is being developed, database structures change often. In MySQL I could select my old data and convert it without much of a hassle. The kind of queries that you can run on App Engine are so limited that the old data and the new data cannot be properly distinguished. In the end, I added a version attribute to all my entities, so that I could later do a "SELECT * WHERE version = '3'" to perform a transition.