-- Last Updated: Sep-26-12 3:55 PM EST --
If you can find a way to attach more tie-downs, that will help. For example If you normally tie a pair of tie-downs to each end, supplement those with another pair tied to the first thwart away from each end. Ropes tied in that way, closer to the center of the boat, will be much more effective at supplying lateral force to resist the tendency of the boat to twist or slide sideways. Among all these various ropes, make sure there's a pair at the front and back which OPPOSE each other, so that whether the boat "attempts" to slide forward OR backward that one pair of ropes opposes that action. Lots of people arrange their end tie-downs so that both sets resist movement of the boat in one direction, while neither set opposes boat movement in the other direction (don't do it that way).
The advice already provided about positioning the boat behind center (with respect to the roof, not the entire car) is very good. A canoe who's center point is about three feet behind the center of its contact area (with roof or roof rack) will be MUCH less prone to getting turned cockeyed by cross winds. On the other hand, centering the canoe relative to the length of the whole car (rather than just the support area) puts greater length ahead of the supports than behind them, and that's a horrendous situation in cross winds (yet lots of people do it that way).
Of course, the big problem with all this advice is that most cars don't have convenient anchor points for tie-downs. On most cars, simply finding good places to tie ropes will be the hardest thing of all.