I have a dark brown rub rail and I matched it pretty close with a high quality silicone caulk. I did top & bottom so that everything is sealed up completely. I taped it off to keep the gelcoat clean. I also cleaned it with acetone on a rag first to ensure a good bond - got down into the gap as well as I could. I pulled the tape when the caulk skinned over - I was afraid of the tape sticking in the caulk if I let it cure completely. Worked out well. It's been about two years and it still looks good. I can't remember what product I used but I am sure it was a marine silicone caulk. Sealants are stronger but this is really more of a job for caulk since it is an exposed finish.
Let us know how it works out for you and take a few pictures - I think lots of boats could benefit from this simple little cosmetic project.
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