Clicking sound when braking - '97 SW1 w/Man. Trans.

While moving and applying the brakes, I'm getting a clicking sound out of the transmission. It sounds like something is loose and clicks once every wheel revolution. At first I thought it was the brakes, but it isn't. With the car on jack stands, only the left wheel rotates until I apply the brakes slightly. That's when the clicking seems to start. Any ideas?

CV joint(s) most likely, but how many miles on it? Could be a wheel baring as well. Does it get worst when you turn the wheel rite or left or it does not matter?

CV joint(s) most likely, but how many miles on it? Could be a wheel baring as well. Does it get worst when you turn the wheel rite or left or it does not matter?
I just replaced both front wheel bearings, so it's not that. The sound is coming from inside of the transmission, not from the CV joints. I've been told that the differential applies power to the wheel with the least resistance. Since the clicking occurs only when I apply the brakes and even out the resistance, I'm thinking that it has something to do with the differential.

Not a good sign. Check the differential pin :

http://www.youtube.com/watch?v=-gqhGC5vKDY

This is what a bad one looks like:
http://www.youtube.com/watch?v=r2us1JT_vRY