AFAIK:
Gold is calculated based on the distance (with naval routes being worth more than land routes) and the base amount being based on resource difference between both cities (so the more diverse resources they have, the better the profit).
Science is calculated based on a number of techs one side has that the other does not (rather than flat science development difference). So, if one party is beelining into one side of the tech tree and the other into another side, they will both get science boost from the trade.
Religion flows along the trade route if the trade route is set between cities that are too far away to religiously pressure each other by normal means. The amount of religion flowing via a trade route is then calculated normally, as if the cities were within each other's normal pressure range.
I don't believe you can get Culture from a trade route.