Movies sometime lag on my 15" MacBook Pro (2011)
I had this same problem and had already installed perian as suggested above. This seems to be a frequent problem, I've had read the explanation but it's a long time ago so don't ask me anymore what the cause is.
I fixed it with 'Niceplayer' this player can preform a pre buffer. So if you load in a large mkv file for example with nice player you'll see a small white line going across let the loading complete (goes fairly quick) and press play. No more lag :) at least for me.. Hope it'll help you too...