With apachetop you can monitor which URL's are accessed how many times and what the Apache processes are doing.
http://www.howtogeek.com/howto/ubunt...ith-apachetop/
Or the favorite search engine of your choice might help too. Additionally you can enable mod_status - just temporary - to know a bit better what is taking so long e.g. running a PHP script.
With tuning-primer / mysqltuner you can change the values of your DB to match your needs like tuning Caches as example.
Finally - with OS tools like lsof you can watch opened files abd what processes are doing all the time.