NFC is a great technology but has been crippled on Windows Phone by the need to confirm each action, making the touch-less technology rather pointless.
Windows Phone 8.1 has finally fixed the implementation, with users able to specify an app as Trusted.
Unfortunately it can not be done ahead of time, and as far as I know does not work for NFC transfer between devices.
Apps are designated as trusted after you tap an NFC tag which activate the tag, but not on the first go, but only after the second tap. This should prevent users from randomly trusted a tag they only access once.
Once an app is marked as trusted, it will show up in the NFC settings under Apps I Trust. Users are able to tap and hold these apps and then remove them from the list later.
While this does fix the biggest issue with NFC on Windows Phone, the next issue is the lack of automation in the OS, preventing an app for example from putting your phone on vibrate and activating WIFI when you get home. For this we may have to wait for Windows Phone 10.