I have developed JEE website on GAE couples of time. I want to share my experience of it.
My website based on springframework 3.
GAE BigTable's JDO interface is really good. I use it as ordinary relation database.
I design the Entity Object just like relation database's table.
Each table have at least 2 columns, named "key" and "id", key for BigTable, id for
my app.
Backup and restore data, we can use low level API
Seach Engine, Compass is good to support GAE
Bind my own domain name to this webapp
Write a RPCService for Ajax