Store list of configuration files paths
After working with systems for a while, you simply know the paths. You know global settings are most likely to be in /etc/<applicationname>, you know your log files are in /var/log, you know you live in /home/mike.
These paths will get second nature to you. And they better should.
Store list of handy commands
Go over to commandlinefu and create a list of your favorites.
Also, once you know your paths, you might not even need to write down stuff like your example.
You know you like nano for editing, you know you want to edit the PHP settings for Apache, so it's nano /etc/php/apache/php.conf or something like that. But that isn't the right path, is it? So use tab-completion to get the real one:
nano /etc/php/apa<tab>
nano /etc/php/apache2/php<tab>
nano /etc/php/apache2/php.ini
And there we go.
Store list of server properties (hardware, location etc.)
Do it however you like it. Create a Wiki. A plaintext file if you like that better. Just do it.
Also, try to learn how to extract that information from a machine if you need to get it quickly. A quick lspci or ip a or route -n or cat /etc/*-release or uname -a can be all you really need at times.
Monitoring Tools
In my opinion, the go-to monitoring tool is Cacti. It's weird to set up, but there are quite a few tutorials on the web. It can monitor all the metrics you noted in your comments (and many more):

alias phpini='nano /etc/php/apache2/php.ini'. – slhck♦ Mar 8 '12 at 11:34