I have configured php with the following command:
./configure \\
--prefix=/opt/phpfcgi-5.3.28 \\
--with-pdo-pgsql \\
--with-zlib-dir \\
--with-freetype-dir=/usr/
If you got that message, even if you installed libfreetype6-dev, then try this:
mkdir /usr/include/freetype2/freetype
ln -s /usr/include/freetype2/freetype.h /usr/include/freetype2/freetype/freetype.h
After this, do .configure again.
Additional hint: For some Systems you have to use /usr/local/include....