Copper, Silk, Dyes, Citrus, Gems, spices, Trouffles, Cotton, Sugar, Fur and Salt. These are the bonus resources that is not directly affected by a special building(like gold and silver are by the mint). Whales, Pearls and Crabs get a bonus from the 'Harbor' and 'Sea port' building.
1. Copper should get +1 hammer from the forge building, like iron does already
2. Trouffles and spices should get a +1 gold from the operahouse building, as rich people likes an expensive dinner before they see a show.
3. Cotton, Silk, dyes and furs should get a +1 hammer or gold bonus from a 'Textile mill' building that could be built when you research "Economics".
4. Citrus and salt should get a +1 gold bonus from the 'Sea port' building as citrus was/is vital for combatting scurvy on long sea voyages. Salt was/is important for conserving food on long voyages as well.
5. Sugar, and perhaps wheat, should get +1 gold from a 'distillery' or 'brewery' building.
6. Gems and Pearls should get a bonus from a 'jeweler' building(this one is a little sketchy)
7. I came up with a good suggestion(according to myself) for a new building and tech. A 'Meat cannery' building where food is processed and packed into cans. Should give a bonus to cattle, sheep and fish(maybe crabs, whales and other aswell). This building will then be available with a 'Pastuerization' tech that should be place between the 'Biology' and 'Refrigeration' tech.
I'll shut up now