MySQL my.cnf performance tuning recommendations

Try starting with the Percona wizard and comparing their recommendations against your current settings one by one. Don't worry there aren't as many applicable settings as you might think.

https://tools.percona.com/wizard

Update circa 2020: Sorry, this tool reached it's end of life: https://www.percona.com/blog/2019/04/22/end-of-life-query-analyzer-and-mysql-configuration-generator/

Everyone points to key_buffer_size first which you have addressed. With 96GB memory I'd be wary of any tiny default value (likely to be only 96M!).

I tried this tool and it gave me good results.

https://github.com/major/MySQLTuner-perl