I like 'em on the inside:
...because I like the hand positioning when I'm gripping the brake hoods. With them set up like this, I get an upright, wide riding position with hands on the outside/ends of the bars; a less bent, but still angled position riding with my hands up in the hooks (80% of my riding); and a slightly more aero and forward position when gripping the brake hoods. The brakes work well where they are for me since I spend so much time with hands up front of the bars--I can easily reach the levers from that position, and the brakes would actually be in the way if they were on the outside of the bars.
Figure out how you're going to use them and where your hands are going to be most of the time. On the outside flats? Place the brakes on the outside of the bars. Up front in the hooks? Brakes go more toward the inside.
Here's some reading (link from Sheldon's Harris Cyclery site):
http://www.stanford.edu/~dru/moustache.html