The one thing that I want to preserve across upgrades that is not kept in /home is my crontab, which lives in /var/spool/cron. Occasionally I would forget to grab a copy of my crontab before upgrading, and then I'd be sad.
It finally occurred to me that I should keep an up-to-date copy of my crontab in my home directory. And what better way to do that than with cron itself. Here's what I have in my crontab now:
00 03 * * * /bin/crontab -l > $HOME/.crontab-${USER}-backup
Now I always have a recent backup of my crontab in my home directory, and I never have to worry about losing it during an upgrade.