MSAA is pretty much dependent on the GPU of your Computer. It will vary game to game, though, you can safely say that increasing MSAA from 2x to 8x increases load on GPU, and puts no extra load on the CPU.
Morphological anti-aliasing, MLAA, introduced by Intel, on the other-hand, does AA putting load on the CPU.
The massive stuttering you experience, is due inconsistenciy in "Maximum Pre-Rendered Frames" value, as enforced by your GPU, and the game engine.
So if you put the value to 5 in the Control Panel, and the game Engine puts it to 2, you experience lag. On games like Far Cry 3, where you can choose the number of pre-rendered frames, you should make sure that the in-game value is same as that you set on N-Vidia Control Panel.
In other games, you should keep it to "Application Controlled", or you can put lower values to lower demands off the system.