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. I'll try to find or make up-to-date fixed versions shortly.