What is the recommended directory to store website content?

There is no "best" directory. And while people might argue that this question is subjective, or that the actual placement of files does not matter—and they're right about the latter—there are standardized recommendations on where to put what in Unix-like systems.

The Filesystem Hierarchy Standard defines this and offers you the following:

• /var – a place to put data that changes during normal operation, like logs, etc. /var/www is the default directory to place web content for Apache, but its usage is not standardized at all and just the "usual" place you'd put it because people don't change the default settings very often.

• /srv – this directory should contain data that is served by the system. This is usually the place you want. The FHS explains:

  This main purpose of specifying this is so that users may find the location of the data files for particular service, and so that services which require a single tree for readonly data, writable data and scripts (such as cgi scripts) can be reasonably placed. Data that is only of interest to a specific user should go in that users’ home directory. (…)

  One method for structuring data under /srv is by protocol, eg. ftp, rsync, www, and cvs

  So, simply create a /srv/www directory and use this. You can create subfolders for every virtual host you might want to serve with your machine.

• /home contains files that really should just belong to one user. Apache for example allows userdirs, so you can access a user's web files through http://example.com/~username, and they're served from the public_html directory in the user's home.

  If you use a server that is shared among multiple people, and you want to allow everybody to host their own scripts, this is where they should go. Remember to make the directories writable by the user they belong to only.

In essence /srv/www and /var/www are directories you should create subdirectories in for any web project you might want to host. You can then define different permissions on these directories to allow certain users or user groups to write to them. If you have projects for one user at a time, use /home.

Well you can put files anywhere long as things can access them properly, however cluttered filesystems are a headache if someone comes in later.

/srv is most logical plus if you follow Filesystem Hierarchy Standard it would go here.

If you do multiple domains you can do /srv/domain1 /srv/domain2 etc etc then subfolder out inside there /ftp /www /tftp /logs /etc.etc.etc

To me that feels a very solid structure to build upon and easily control

But as an administrator you can do as clean or messy as you wish.

Ok easy quick answer.

If your web files on the system will only be accessed by ONE user on the linux system. Use the home directory of the user (~/).

If your web files on the system will be accessed by MULTIPLE users on the linux system. Use /srv/.

This is exactly what http://refspecs.linuxfoundation.org/FHS_2.3/fhs-2.3.html#SRVDATAFORSERVICESPROVIDEDBYSYSTEM states.

Here is the quote:

/srv contains site-specific data which is served by this system.

This main purpose of specifying this is so that users may find the location of the data files for particular service, and so that services which require a single tree for readonly data, writable data and scripts (such as cgi scripts) can be reasonably placed. Data that is only of interest to a specific user should go in that users' home directory.

Bonus: www? ftp? Organize by protocol? Huh?

As stated here in http://refspecs.linuxfoundation.org/FHS_2.3/fhs-2.3.html#SRVDATAFORSERVICESPROVIDEDBYSYSTEM

• If your website is only accessed by ONE user on the system and ONLY via the browser (http protocol) then: ~/http/your-website-directory/
• If your website is only accessed by ONE user on the system and NOT ONLY via the browser but multiple protocols (i.g. http AND tcp AND ...) then: ~/your-website-directory/
• If your website is accessed by MULTIPLE users on the system and ONLY via the browser (http protocol) then: /srv/http/your-website-directory/
• If your website is accessed by MULTIPLE users on the system and NOT ONLY via the browser but multiple protocols (i.g. http AND ftp AND ...) then: /srv/your-website-directory/

Huh why not www? This is legacy from the Apache time. www doesn't specify which protocol is being used. Debian still uses this as of today while for example Arch linux uses /srv/http.