I don't know your requirements or your apps, but this isn't a quick answer type of question. I'm very interested to see what others have to say. However, I have a suggestion that may or may not work for you, depending on your requirements and situation. particularly, this will not help if your users need to use the app even when the network is unavailable (offline access).
Keeping a bunch of small databases synchronized is a fairly complex task to do correctly. Is there any possibility of just having one centralized database, and either having the client applications connect directly to it or (my preferred solution) write some web services to handle accessing/updating data rather than having a bunch of client databases?
I realize this limits offline access, but there are various caching strategies you can use. (Which of course, leads you back to your original question.)