I'd like to know if anybody has found either the cause of, or solution to this problem.
I also have a '04 Cannondale Cyclocross 800 with the cantilever brakes, and like the others here, my front brakes have shuddered (to the point of danger in traffic) ever since the bike was new as well.
Over time, I've tried adjusting and finetuning the brake setup myself, changed brakepads, and 3 different bike store mechanics have had a go at fixing the problem as well. Nothing has worked *except* regular applications of 'Ezy-Glide' dry lubricant (yeah, I know) - that makes the brakes perfect: no squealing or shuddering, just smooth progressive braking power.
It feels like the brakes are grabbing so powerfully that indeed the whole fork is flexing, and that the lubricant is what's required to 'ease them up' to the point where the fork shudder doesn't set in. Or maybe it's the wheels - it's kind of hard to tell when you're on the bike.
The wheel is true, and everything in the headset is tight and adjusted, so it's unlikely to be caused by those two potential issues.
If anybody's found a solution that's less ridiculous than squirting EzyGlide onto the pads and wheel every week, I'd love to hear it... or is it just that MTB cantilever brakes and flexible roadie carbon forks just don't match.