Ask HN: What are your (web) server setup conventions?

I'm doing freelance projects and sometimes have to host my sites. I'm really lost as to how I should organize everything though. I've just set up a new slice and I want to ask the community how, apart from the "apt-get install" commands, people organize and set up their servers.

1. Is the /usr/local directory good for anything?

2. Where do you stick site code?

3. Where do you stick user submitted content?

4. Where do you stick custom compiled binaries?

5. Any other tips or conventions you want to share?