It's really up to you. I never use the global include directory (if I can even remember where I put it!); I define my include_path at runtime:
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ini_set('include_path', ini_get('include_path') . ":$GLOBALS[PATH_PREFIX]/$GLOBALS[PATH_CORE]:$GLOBALS[PATH_PREFIX]/$GLOBALS[PATH_TEMPLATE]");
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Of course, I develop apps designed to be deployed to separate servers, so it doesn't really make any sense for me to use a global include directory.
On the other hand, if you had several projects, and you were going to serve them all from the same machine, it would save you some hard drive space if you only had to keep one copy of each redundant file. Plus, if you had to make changes to one of those files, you wouldn't have to worry about propagating the changes to six other copies (but then, you DO use version control, right?)
Incidentally, although this is not specific to the PHP/Includes folder, if you store include files outside your site root, they can't be accessed except via include (ok, and require) statements inside your code. E.g., you could store your MySQL login script here so that nobody could access it directly.