MPlayer can play them as well, and in my experience it's a bit faster and smoother than VLC. The problem is that the MPlayer GUI is not very reliable, and often doesn't work at all. I actually compiled my own MPlayer command-line version from source, and I use that frequently now. If you have Apple's developer tools installed, it's really not hard.
I've heard that VLC and MPlayer (and I suppose Perian, since it's based on the same core) do not use multiple threads for video decoding at this point. That means the second core of your processor would basically sit idle. (That could be out of date or just plain wrong, though; can't say I've ever tested it.) Apple's H.264 decoder is threaded, but I don't think there's any way you'll be able to use it with an mkv. Hmm.