I have been trying out RDS for a few months and here are some issues I have:
Using SQL profiler is tricky. Since you cannot connect profiler directly to the server, you have to run some stored procedures to create a log file that you can analyze. While they offer some suggestions about how that is done, it is far from user friendly. I would only recommend that you have a certified SQL professional do this kind of work.
while Amazon backs up your instance, you cannot restore an individual database. I have a web app with several separate customer-specific databases and my solution was to launch an EC2 instance with SQL running on it to attach to the production RDB database and import the data and then back it up on the EC2 instance. The other solution was to use a 3rd party tool that creates a massive SQL script (on the app server) that will recreate the schema and populate the data back to a restore point.
