Since I walk to work, I use my car for canoeing for much of its mileage.  It's not unusual for me to go on 1000-3000 mile trips with several boats on the car.  Consequently, I made my own roof rack that would be adequate for the load.  With a large canoe, it's not so much the weight, but the wind pressure that come from strong cross-winds.  It's sometimes quite scary!

The crossbars are made from 1" square steel tubing with feet that triangulate to the runner on the roof.  Two bolts hold each foot to the base.

Roof rack

The "runners" are made from an aluminum T extrusion that's bent to follow the roof contour.  Each piece is fastened to the roof panel with 18 threaded inserts, put into the roof panel very carefully.  I also have a thin piece of rubber padding between the extrusion and the paint.  So far, through many, many days of rain, it hasn't leaked.