Cliff Jacobson has written extensively about modifying canoes.  Here's what I've done:
- Replaced the stock curved cane seat with a wide-cane seat in my Mad River Independence.  I usually sit off-center and the wider cane is much more comfy.
- Moved the seat back 8 inches to counterbalance my main pack on BWCA trips.  This meant getting a different seat because the boat is narrower behind the stock seat position.  I'll be doing this mod to my Blackhawk Ariel this spring.
- Removed the stock tractor seat from my Wenonah Prism and install an adjustable cane seat.
- Installed 2-inch longer thwarts in my Bell Royalex Wildfire (now called the Yellowstone Solo) to improve both primary and secondary stability.  Move the main thwarts 5 inches toward the center and installed two additional thwarts between the main thwarts and the carry thwarts.  This made the hull fairly rigid, since the stock vinyl gunwales are pretty soft, more like willowy.  Also installed kneeling pads, thigh straps and flotation bags for up to Class II+ whitewater.
- Installed parachute cord lashing points in my Wenonah Sundowner for carrying paddles and other stuff.
- Installed skid plates on Rx Wildfire and Prism.

I've probably done more stuff but I can't remember all the details.