I would have your 50 virtual hosts all using the same DocumentRoot. That way you guarantee that all sites will be using the same common files.

To pick up different css and image directories, use the Alias directive to point to explict directories for each VirtualHost.

The most obvious solution, assuming that all the different sites are hosted on the same server/filesystem, would be something akin to:

+- common files (outside web root)
|
+- httpdocs (web root)
   |
   +--+- website 1 specific files
   |      |
   |      +- images (etc)
   |
   +--+- website 2 specific files
          |
          +- images (etc)

With the above diagram, all you need to do is include the relevant files from the shared location, and override/overrule for the purposes of site specificity using the site-specific files (whether stored inside, or outside, of the web-root).

If your sites are all hosted across different servers then it gets a little more complicated, since any common files would have to be hosted somewhere in the web-root (accessible via http). This isn t ideal, though there s nothing stopping it working, but in terms of bandwidth usage and issues with cross-site security, it s likely to be problematic.

With Virtual Hosts, you re at something of a halfway house between the two options; so long as they can all access the same document root you re still able to use the includes (as suggested by dland elsewhere in these answers).

If these sites are all on the same server, you can just include the files in your php includes.

then you can just include them as if they were in the same directory as your current php file.

I think you can just #include the files that you need from the main folder, you will have to make it accessible from all the sites (using soft links will cause the server to think they are in each site s directory)

Using soft links will make it easier from the paths concerns, and you won t need to use paths "outside" your httpdocs directory.

If they re on the same server, you could just symbolic link the files:

ln -s /home/ftpuser/public_html/commonfile1.php /home/ftpuser/public_html/commonfile2.php

This breaks down in a shared hosting setup where different users (file owners) are involved.