You may want to keep updating in mind. If you keep the OS (/etc, /boot, /usr, /opt, /var for example) separate from the area in which you keep your data such as /home and maybe /srv (assuming your DBs such as MySQL and PostgreSQL don't seat themselves somewhere in /var) it allows you to do an install from scrach without destroying your data.
That doesn't mean you shouldn't back up :-), but it save a lot of time during system upgrades as you just don't bring your data partition online until post upgrade.
Be careful with user home directories, though. Especially if you change distro you may need to create a template user and look at the app defaults before you override them with those of a previous setup..