Patching

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It should be noted that "dependancy hell" is usually because the SysAdmin has installed packages from different distributions. For example, installing SuSE packages on a RedHat system is asking for trouble. Packages built for a specific RedHat version almost always work, as do packages rebuilt from .src.rpm files. (RedHat and other RPM-based systems are quite a bit nicer once you learn to roll your own RPM .spec files)

Debian

Using Debian GNU/Linux or any of the ubuntu variants, it's as simple as

apt-get update
apt-get dist-upgrade

and all of your installed applications will now be up to date. You can modify where you get your updates from the /etc/apt/sources.list file.

FreeBSD

I've created two shell scripts which I've named update, and upgrade. You will need portsnap, portaudit and portupgrade installed to use these:

 #!/bin/sh
 # update
 /usr/local/sbin/portsnap fetch