As far as I know there isn't a well accepted set of best practices for MySQL, but there are many best practices known and used by most MySQL DBA's. One of those best practices is that the datadir must not be equal to a mountpoint; it has to be a subdirectory of a mountpoint. I learned this the hard way a few years ago when I used a NetApp Filer via NFS as a data directory. The NetApp filer exposed the snapshots via a .snapshot directory. A database in MySQL is a directory, so MySQL thought that the .snapshot directory was a database. This resulted in some issues with our monitoring scripts, so we had to create a mysql_data directory and move all the databases to that directory. For other setups directories like lost+found, .zfs, etc. gave similar issues. In MySQL 5.6 a new feature was introduced to make it possible to make some databases hidden. To do this a ignore-db-dir option needs to be specified for each directory. On a running server the list of ignored database direc...

The recently released MySQL 5.6 gets a lot of attention, but for those who are still on 5.5 there is also good news: There are two new features in 5.5. The first feature is that there are more INFORMATION_SCHEMA tables for InnoDB. This means that it's possible to 'see' what's in the buffer pool. It also makes it possible to get more information about the LRU list. From the 5.5.28 changelog : InnoDB: Certain information_schema tables originally introduced in MySQL 5.6 are now also available in MySQL 5.5 and MySQL 5.1: INNODB_BUFFER_PAGE , INNODB_BUFFER_PAGE_LRU , and INNODB_BUFFER_POOL_STATS . (Bug #13113026) This is in the "Bugs Fixed" section instead of the "Functionality Added or Changed" section, which is a bit weird in my opinion. The second feature is a variable which makes it possible to get more information about the deadlocks. From the 5.5.30 changelog : InnoDB: The innodb_print_all_deadlocks configuration option from MySQL 5.6 ...