How do you organize your $HOME?
yan: my homedir is organized as follows:  bin/ - binaries that aren't installed; appended to $PATH
  docs/ - docs for what i'm working on is here
  src/ - code
    dl/  - that i downloaded
    */ - that i wrote
  misc/ - self explanatory
  notes/ - todos, notes i jotted down, urls
  tmp/ - my sandbox usually filled with downloads, tmp.c and the like

And OS X's dirs like Library, Documnets, etc