NetworkPoints is a very simple to use system. With a developer API to allow for easy integration into minigames, as well as a useful command system to modify the users points ingame via commands, NetworkPoints is the way to go.
Please note, NetworkPoints depends on MineSQL. http://dev.bukkit.org/bukkit-plugins/minesqlapi/
/points get [player]
/points add (player) (amount)
/points subtract (player) (amount)
/points set (player) (amount)
If you are an existing/new server, NetworkPoints, is, in my opinion, the easiest way for both your developers and administrators to easily and efficiently modify a users points. From a developer's standpoint, NetworkPoints takes only 1 line of code to modify a users value, while other systems, like Vault, take more setup and understanding.
When NOT to use NetworkPoints...
If you are an existing server with no dedicated developer who is willing to integrate, and are dependent on 3rd party plugins who implement another system (i.e, Vault), NetworkPoints will be significantly harder for you to switch to.
MySQL point system with easy API