Lot of things the author mentions isn't valid for practical world. Apache (with TLS/SSL) with /dev/random is asking for trouble; meaning, client's requests will just block forever if not enough seed cannot be generated (same with TLS/SSL aware postfix).
A lot of software out there in use that require real-world RNG thus default to /dev/urandom. I am not sure whether its good or bad.
I know that on osx atleast, Yarrow kind of shields the fact that /dev/urandom and /dev/random produce non-blocking RNG.
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.
I know that on osx atleast, Yarrow kind of shields the fact that /dev/urandom and /dev/random produce non-blocking RNG.