I use/upgraded to MySQL 5.0.22 and the only trouble I have had is talked about here:
MySQL Password Hash's
I fixed it accoring to that article and things have been cosy ever since. I love using 5.0 and all it's first party tools (Admin, Query Browser, and the Tray Monitor) though. Also make sure you make all the SQL command updates in the readme's for the current emulator version. If you are not comfortable with doing all the little database commands I suggest sticking with the earlier version. If ya do though, back everything up and keep a fallback postion every step of the way like I did.
