Some tools of note here: ossec, alienvault ossiem, selinux, pf, iptables etc. what you need is a hids, system accounting, and hardened os (proper acls, selinux, upto date binaries, firewalls etc).

Log correlation helps too. Oh and chuck in notifications for all the above (e-mail, pager etc.) and I think you should be set for future. But please remember, these are not silver bullet.