A lot of PHP applications that I've worked on that allow file uploads place the files into a directory that is publicly accessible, this isn't a problem so long as your upload script never ever allows scripts to be uploaded.

It doesn't matter how good you think your MIME type or extension filtering is why allow the PHP interpreter near the files you never expect to be interpreted?

Disabling The PHP Interpreter

There is a php_engine directive that Apache exposes, it can be used in both .htaccess files and the main Apache config, this directive tells the PHP interpreter to just not run.

Usefully this can be placed in a Directory or DirectoryMatch block. This effectively allows us to sandboxing a directory, uploads for example.

Disabling File Handlers

Next we tell Apache to handle all files the same, as though they were static content that doesn't need interpreting.

SetHandler none
SetHandler default-handler
RemoveHandler .cgi .php .php3 .php4 .php5 .phtml .pl .py .pyc .pyo
RemoveType .cgi .php .php3 .php4 .php5 .phtml .pl .py .pyc .pyo

Disabling Overrides

As these settings can be defined in an .htaccess we also prevent Apache reading any .htaccess files in the directory we are sandboxing. This prevents malicious .htaccess files disabling all protection we've added.

This is easily done by setting the AllowOverride directive to None.

Put It All Together

<DirectoryMatch ^/path/to/(one|many)/directories>
    AllowOverride None

    SetHandler none
    SetHandler default-handler

    Options -ExecCGI
    php_flag engine off
    RemoveHandler .cgi .php .php3 .php4 .php5 .phtml .pl .py .pyc .pyo
    RemoveType .cgi .php .php3 .php4 .php5 .phtml .pl .py .pyc .pyo
    <Files *>
        SetHandler none
        SetHandler default-handler

        Options -ExecCGI
        php_flag engine off
        RemoveHandler .cgi .php .php3 .php4 .php5 .phtml .pl .py .pyc .pyo
        RemoveType .cgi .php .php3 .php4 .php5 .phtml .pl .py .pyc .pyo
    </Files>
</DirectoryMatch>