A quick update can be done by

apt-get update
apt-get upgrade

For general installation, updates, and so on

aptitude

is a good choice.

Anything that shouldn't be updated? Like stuff with custom patches? Does apt have a history of clobbering configs or anything?

Also, magic commands

Anything tied to specific kernel versions?

The stock Debian stable kernels have a bug in the serial drivers that make the console on Ultra 5s unusable. We previously fixed this with a slightly later version of the package (2.6.8-16), but it looks like the security update (2.6.8-15sarge1) should have the console fix, along with a bunch of security fixes. I haven't tested this version yet.