At the moment, my top 3 tools to tune MySQL are:
- mysqlreport: a friendly report about the status of your MySQL server (or
SHOW STATUSfor real persons);
- innotop: a top-like program to see what's going on with your MySQL server (works with multiple servers);
- mysqlsla: analyses MySQL statement logs (including slow queries).
Other tools are also useful sometimes:
- Duplicate Index Checker: checks your indexes to see if you have multiple indexes covering the same information, in the same order;
- MySQL Query Profiler: reports on what work MySQL will have to do for a given batch of queries.
I discover most of this tools reading the Xaprb blog, recommended.