MySQL Replication using SSL
It's a problem in public websites because you can't email your shiny new CA key to everybody on the Internet.  So instead by convention browsers ship with a small list of CAs (Verisign and friends) and we all buy certificates from them.

In database replication, you can visit both servers and install your new CA key.  As long as you trust you, and you don't want strangers to authenticate to your database, you're probably in the clear.