I like to keep things clean and separated on my systems:
- / and /usr are for the OS
- /usr/local is for stuff installed via ports/packages
- /opt is for stuff I compile/install by hand
Everything is kept separate, there's no chance of anything I install messing things up with the system, and it's a simple "newfs /opt" to uninstall everything.
Of course, as the admin for my systems, I can make up whatever rules I like.