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My tendency would be one of:
1. If I'm hosting one or more sites, but adminning them myself, a structure under /srv for the pages, media, and DB files (if any).
2. If I providing hosting to joe the user, I'd set them up under /home/joe.
I wouldn't mess around under /usr, since most package systems assume they own it (which is why I don't like /var/www, either). Of course, /usr/local/* is yours.
If you're uploading media via the webserver (like a picture gallery, or user forum icons, or some such), it should definitely be in its own directory, with appropriate permissions.
For backups, I don't backup stuff that I can re-install with apt-get. I *do* backup configuration files, though (all of /etc, basically). One important bit to backup is the list of installed packages; in a Debian based system, get /var/backups for several good things. Actually, /var is tricky, there's lots of big things you don't need backed up, ususally, but picking and choosing is a pain. For example, you *might* not want /var/log, depending on how you feel about log files, and /var/cache, which by definition can be rebuilt. Since I don't put any local stuff under /usr, I don't back it up.
_________________ The irony is that Bill Gates claims to be making a stable operating system and Linus Torvalds claims to be trying to take over the world.
-- seen on the net
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