Yes, I have a dark secret: my /home / /var is all on the same partition! I'm changing this with a clean install of ubuntu 12.04 with multiple partitions. Besides my scheduled /home backups, this is a list of other things to back up on an external hard drive before my clean install.

gistfile1.txt

sources.lst (for apt-get) 
cp -r /etc/apt/ ~/aptsrcs/

fstab file (for automatically mounting my external HD on boot). 

wireless settings 
cp -r /etc/NetworkManager/ destination
http://askubuntu.com/questions/212299/how-migrate-my-keyring-containing-ssh-passprases-nautilus-remote-filesystem-p

also: (already backed up). 
cp -r ~/.gnome2/keyrings destination

my postgis databases for each or just write a bash script to them all. 
pgdump nameofdb > nameyourdumpwhateveryoudlike (see: http://www.postgresql.org/docs/9.1/static/backup-dump.html)

better yet dump_all > mydumps

list of the packages that you have installed. 

( zcat $( ls -tr /var/log/apt/history.log*.gz ) ; cat /var/log/apt/history.log ) | egrep '^(Start-Date:|Commandline:)' | grep -v aptdaemon | egrep '^Commandline:'

- a list of packages (no dependencies) that you explicitly installed. seems a little low. 

dpkg --get-selections > packagesihaveinstalled
http://askubuntu.com/questions/17823/how-to-list-all-installed-packages

git repos (is a simple cp -R sufficient ?)