Ye Olde Extra Secret Canoelover Miracle Gunwale Elixir works wonders. No stain, just the natural color of the wood (white oak).
This leads me to the lecture part of this post.
Some of you own canoes. Some of you own canoes with wood gunwales. A small percentage of you wood-gunwale-canoe owners lets them go until the substance holding the boat together is barely recognizable as a wood product.
While I can give your gunwales the canoe equivalent of a four-way cardiac bypass, why not just keep your gunwales in good shape to start with? Ask any Public Health Nurse what's the best way to treat a disease, and she'll always answer "Don't get it in the first place." N.B. I say "she" because I've never known a male Public Health Nurse. Go figure.
Be good to your wood,