Usually, in all games with AA options, i use these - assuming they are optimized for the game.
In older games & sims (FSX for example) i use nvidia to fine tune AA settings, which is a lot better than the ingame options.

In case of WOFF, i was playing with the nvidia AA settings which reduced my FPS to 15. Now i gave it back to application controlled and it runs fine.

It depends on the game. The newer, the more i keep the ingame AA.