One of the less documented tuning parameters I found is the threa dcache size. Normally it is a very small value for the number of simultaneous connections you likely support. Increasing it can result in elimination of random pauses/slowdowns.

In general, it is impossible to "tune MySQL" though. You can allow it to use more system resources and in some cases you can get it to be less durable to gain write performance, but to get orders of magnitude increases you need to restructure your data. Try sharing or partitioning data. Increase or reduce the number of indecies. Denormalize data. Archive logs to flat files. Put the OS, /var/lib, and /var/log on separate physical drives. Run MySQL on bare metal since disk IO is often a bottleneck and virtualization can add overhead. Restructure the data. At one point a write heavy app I was optimizing was logging things to the database (that needed to be queries). Each log entry contained extra data we did not query. One speed up that worked was throwing the majority of the extra data into a single gzipped JSON blob. This made it easier for MySQL to fetch fewer pages. Less IO, faster operation.