Looking to use Pi3 as a webserver (Apache, PHP, MySQL). I need it to allow other devices to connect to it via WiFi to access the hosted web site, Is WiFi-Direct the best way of doing this as there is no router, if so are there any instruction on how to do it?
I think the most straighforward way to achieve your goal would be to setup your Raspberry Pi as an access point. I would suggest you follow the official how-to from the Raspberry Pi foundation.
As your Raspberry Pi is standalone and no routing is needed, you can stop before the part ADD ROUTING AND MASQUERADE of the tutorial.
Now your other devices can simply connect to the SSID you have specified in the
hostapd.conf file, using the passphrase (pre-shared key) defined there.