Here's what I use:

• ~/prj/myproject/trunk
  • bin - cgi-bin stuff
  • conf - config files
  • devdocs - just like it sounds
  • externals - catch-all for support programs
  • logs
  • modules - module hierarchy
  • templates - mostly mimics modules hierarchy
  • updates - sequentially numbered SQL files to update database structure to "current version"
  • install.sh - single command to move everything necessary into "live" /opt/myproject, unlink/relink conf files, reload apache, etc

All under version control (svn), and Trac.

This layout (copped mainly from some CGI-App docs) works well enough for me, but then my current projects aren't particularly large; YMMV

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