Comment by eatmygodetia

~/tmp - desktop and downloads, mounted as tmpfs.

~/usr/text - pdfs and text files with name format author-title, no hierarchy

~/usr/projects - each project, not sorted by language

~/etc - $XDG_CONFIG_HOME

~/etc/bin - shell scripts

~/bin - programs locally installed

~/src - source code repos, built into ~/bin

~/prog - cache and data

I use CVS to store and version everything, and various environment variable, wrapper script, and alias hacks to move as many dotfiles out the way.