Can you please give me some kind a 'check list' to protect my website running on Linux+Apache+PHP+MySQL.
Perhaps just as important is making sure your PHP applications are secure. If you are writing one yoruself, check out some of the information on the web regarding secure PHP programming. If you're using one of the many popular PHP application such as phpBB, Joomla, Drupal etc. make sure you have the latest version. There are automated scripts which actively seek out and exploit security hole in many of these packages.
With most OSS software there is a mailing list you can subscribe to which will send you security bulletins when a new version is release. This way you can stay in touch with what's going on and get alerted when a new update is available.
Don't forget pro-active steps like ensuring you back up your data and content.
Regards,
Jimbob