Tune and Fix Mysql and Apache configuration for a better performance

Hi, I need and experienced SysAdmin. I have a dedicated server running Ubuntu/Apache/Mysql/Bind that I manage that has around 5 working sites, all base in Joomla. I'm the sys admin of the server with 16gb of RAM so resources are not the problem. Suddenly the site has downtime from time to time in a single day. I need to fix it. The server must be online 100% of the time without problems as it used to do. I could track the problem to Bind and sometimes to mysql. Restarting them solves the problem, but this is not a real solution. YOUR GOALS are 1) to track the problems and fix them. 2) Also to tune Mysql and Apaches configuration and cache to get a better performance. I recently disabled Apache's cache because it wasn't working well. I would like to fix this so the loading time goes from 6 seconds to 2 secs or so. I tried to describe the problems the best I could, anything else just ask me.