I run a small web dev firm that does a lot in the way of PHP and JS, like yourself. What we have found works the best for our core library is a copy of Subversion running on our server. This way we all know exactly what the latest version is, and more importantly we can see how it became the latest version (i.e. what changes were made). A lot of tools run with SVN nicely. For instance, Trac talks to a backend copy of SVN and couples it loosely with a wiki and a couple of other things. A lot of hosting providers will also run a copy of SVN for you, like http://networkredux.com/ (We just switched over to them).

Of course, a root level folder on the ftp server can also work.